starting build "50eb4ff2-cc29-4064-849f-943e49dfe19f" FETCHSOURCE BUILD Starting Step #0 Step #0: Already have image (with digest): gcr.io/cloud-builders/git Step #0: Cloning into 'oss-fuzz'... Finished Step #0 Starting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3" Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Already have image (with digest): gcr.io/cloud-builders/docker Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Sending build context to Docker daemon 5.12kB Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Step 1/5 : FROM gcr.io/oss-fuzz-base/base-builder Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": latest: Pulling from oss-fuzz-base/base-builder Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b549f31133a9: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fbd651eef87f: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1213aebcf1ee: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": a060310a2694: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 497216b932c9: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": dbba7edc028b: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b265efe846ed: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 161940763a8b: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": cf5e5e872386: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 07e64dc83e3d: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0736b6e9e3d3: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2aa8d7237534: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 77f0438adcd7: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b4f29f80fb52: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8a13b0c532a1: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 816028f45e91: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": af4a22e37681: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e254a28c4707: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b93f7310e490: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 537b4d73e924: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fb7466f42249: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": caa5e91e8207: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8e5a6791c7a9: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2a27d4021cc9: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 44a0027834cd: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 02ef4a0d7537: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 639adac7267e: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e2c5062b3d7c: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 77f0438adcd7: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b4f29f80fb52: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1664575004c3: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0c12bc59d07a: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8a13b0c532a1: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 33a9985c1ce6: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b93f7310e490: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 816028f45e91: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": eed49b03c9d2: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 296802ba35d9: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": af4a22e37681: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 56d297e5ca51: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": caa5e91e8207: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 4202398c47b7: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e254a28c4707: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 05ac082b9935: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e5eb489f668b: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 3c031922279e: Pulling fs layer Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1664575004c3: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 296802ba35d9: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0c12bc59d07a: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 56d297e5ca51: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 161940763a8b: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8e5a6791c7a9: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 33a9985c1ce6: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 4202398c47b7: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": cf5e5e872386: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": eed49b03c9d2: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2a27d4021cc9: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 537b4d73e924: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 07e64dc83e3d: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 05ac082b9935: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fb7466f42249: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 44a0027834cd: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e5eb489f668b: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 02ef4a0d7537: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0736b6e9e3d3: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 639adac7267e: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 3c031922279e: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2aa8d7237534: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b265efe846ed: Waiting Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1213aebcf1ee: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1213aebcf1ee: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 497216b932c9: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 497216b932c9: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b265efe846ed: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 161940763a8b: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 161940763a8b: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b549f31133a9: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b549f31133a9: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": a060310a2694: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": a060310a2694: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0736b6e9e3d3: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0736b6e9e3d3: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2aa8d7237534: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2aa8d7237534: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 77f0438adcd7: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 77f0438adcd7: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b4f29f80fb52: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b4f29f80fb52: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 816028f45e91: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 816028f45e91: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8a13b0c532a1: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8a13b0c532a1: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 07e64dc83e3d: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 07e64dc83e3d: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fbd651eef87f: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fbd651eef87f: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e254a28c4707: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": af4a22e37681: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": af4a22e37681: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b93f7310e490: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b93f7310e490: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 537b4d73e924: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 537b4d73e924: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fb7466f42249: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fb7466f42249: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": caa5e91e8207: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": caa5e91e8207: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2a27d4021cc9: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2a27d4021cc9: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8e5a6791c7a9: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8e5a6791c7a9: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 44a0027834cd: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 02ef4a0d7537: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 02ef4a0d7537: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b549f31133a9: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 639adac7267e: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e2c5062b3d7c: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e2c5062b3d7c: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1664575004c3: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1664575004c3: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 33a9985c1ce6: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 33a9985c1ce6: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": eed49b03c9d2: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": eed49b03c9d2: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 296802ba35d9: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 296802ba35d9: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0c12bc59d07a: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0c12bc59d07a: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 56d297e5ca51: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 4202398c47b7: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 4202398c47b7: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 05ac082b9935: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": cf5e5e872386: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": cf5e5e872386: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e5eb489f668b: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e5eb489f668b: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 3c031922279e: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 3c031922279e: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": dbba7edc028b: Verifying Checksum Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": dbba7edc028b: Download complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fbd651eef87f: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1213aebcf1ee: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": a060310a2694: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 497216b932c9: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": dbba7edc028b: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b265efe846ed: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 161940763a8b: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": cf5e5e872386: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 07e64dc83e3d: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0736b6e9e3d3: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2aa8d7237534: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 77f0438adcd7: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b4f29f80fb52: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8a13b0c532a1: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 816028f45e91: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": af4a22e37681: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e254a28c4707: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": b93f7310e490: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 537b4d73e924: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": fb7466f42249: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": caa5e91e8207: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 8e5a6791c7a9: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 2a27d4021cc9: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 44a0027834cd: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 02ef4a0d7537: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 639adac7267e: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e2c5062b3d7c: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 1664575004c3: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0c12bc59d07a: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 33a9985c1ce6: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": eed49b03c9d2: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 296802ba35d9: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 56d297e5ca51: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 4202398c47b7: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 05ac082b9935: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": e5eb489f668b: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 3c031922279e: Pull complete Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Digest: sha256:cede7bc2cc2ece182ffb31a0d118e0e3ade537b2ea40803829f19373815bb8f8 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Status: Downloaded newer image for gcr.io/oss-fuzz-base/base-builder:latest Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> e9b8095f6233 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Step 2/5 : RUN apt-get update && apt-get install -y make autoconf automake zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> Running in b7ed3029d7a5 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Hit:1 http://security.ubuntu.com/ubuntu focal-security InRelease Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Hit:2 http://archive.ubuntu.com/ubuntu focal InRelease Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:3 http://archive.ubuntu.com/ubuntu focal-updates InRelease [128 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Hit:4 http://archive.ubuntu.com/ubuntu focal-backports InRelease Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Fetched 128 kB in 1s (238 kB/s) Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Reading package lists... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Reading package lists... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Building dependency tree... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Reading state information... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": make is already the newest version (4.2.1-1.2). Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": make set to manually installed. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": libssl-dev is already the newest version (1.1.1f-1ubuntu2.24). Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": The following additional packages will be installed: Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": bzip2-doc Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Suggested packages: Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": autoconf-archive gnu-standards autoconf-doc libtool gettext libcurl4-doc Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": libssh2-1-dev pkg-config liblzma-doc Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": The following NEW packages will be installed: Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": autoconf automake bzip2-doc libbz2-dev libcurl4-gnutls-dev liblzma-dev Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": zlib1g-dev Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Need to get 1996 kB of archives. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": After this operation, 6950 kB of additional disk space will be used. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 autoconf all 2.69-11.1 [321 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 automake all 1:1.16.1-4ubuntu6 [522 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 bzip2-doc all 1.0.8-2 [501 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 libbz2-dev amd64 1.0.8-2 [30.2 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:5 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcurl4-gnutls-dev amd64 7.68.0-1ubuntu2.25 [320 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu1.5 [155 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 liblzma-dev amd64 5.2.4-1ubuntu1.1 [147 kB] Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": debconf: delaying package configuration, since apt-utils is not installed Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Fetched 1996 kB in 0s (5794 kB/s) Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package autoconf. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17483 files and directories currently installed.) Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../0-autoconf_2.69-11.1_all.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking autoconf (2.69-11.1) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package automake. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../1-automake_1%3a1.16.1-4ubuntu6_all.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking automake (1:1.16.1-4ubuntu6) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package bzip2-doc. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../2-bzip2-doc_1.0.8-2_all.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking bzip2-doc (1.0.8-2) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package libbz2-dev:amd64. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../3-libbz2-dev_1.0.8-2_amd64.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking libbz2-dev:amd64 (1.0.8-2) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package libcurl4-gnutls-dev:amd64. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../4-libcurl4-gnutls-dev_7.68.0-1ubuntu2.25_amd64.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking libcurl4-gnutls-dev:amd64 (7.68.0-1ubuntu2.25) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package zlib1g-dev:amd64. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../5-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu1.5_amd64.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1.5) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Selecting previously unselected package liblzma-dev:amd64. Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Preparing to unpack .../6-liblzma-dev_5.2.4-1ubuntu1.1_amd64.deb ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Unpacking liblzma-dev:amd64 (5.2.4-1ubuntu1.1) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up bzip2-doc (1.0.8-2) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up libcurl4-gnutls-dev:amd64 (7.68.0-1ubuntu2.25) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up autoconf (2.69-11.1) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up liblzma-dev:amd64 (5.2.4-1ubuntu1.1) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1.5) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up libbz2-dev:amd64 (1.0.8-2) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Setting up automake (1:1.16.1-4ubuntu6) ... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": update-alternatives: warning: skip creation of /usr/share/man/man1/automake.1.gz because associated file /usr/share/man/man1/automake-1.16.1.gz (of link group automake) doesn't exist Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": update-alternatives: warning: skip creation of /usr/share/man/man1/aclocal.1.gz because associated file /usr/share/man/man1/aclocal-1.16.1.gz (of link group automake) doesn't exist Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Removing intermediate container b7ed3029d7a5 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> fe835abde6ca Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Step 3/5 : RUN git clone --depth 1 --shallow-submodules --recurse-submodules https://github.com/samtools/htslib.git htslib Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> Running in 3d7aa9a4f644 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Cloning into 'htslib'... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Submodule 'htscodecs' (https://github.com/samtools/htscodecs.git) registered for path 'htscodecs' Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Cloning into '/src/htslib/htscodecs'... Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": From https://github.com/samtools/htscodecs Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": * branch a815cd02bf0bada68800f32bfb0997d40f579026 -> FETCH_HEAD Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Submodule path 'htscodecs': checked out 'a815cd02bf0bada68800f32bfb0997d40f579026' Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Removing intermediate container 3d7aa9a4f644 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> 60c7e37c5226 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Step 4/5 : WORKDIR htslib Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> Running in 2fd7030729bf Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Removing intermediate container 2fd7030729bf Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> 4f239d98eb21 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Step 5/5 : COPY build.sh $SRC/ Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": ---> 7b3202de1b36 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Successfully built 7b3202de1b36 Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Successfully tagged gcr.io/oss-fuzz/htslib:latest Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3": Successfully tagged us-central1-docker.pkg.dev/oss-fuzz/unsafe/htslib:latest Finished Step #1 - "build-c5d9b30f-062d-4a5e-b44c-af52bd8ba1c3" Starting Step #2 - "srcmap" Step #2 - "srcmap": Already have image: gcr.io/oss-fuzz/htslib Step #2 - "srcmap": ++ tempfile Step #2 - "srcmap": + SRCMAP=/tmp/filePSYvuM Step #2 - "srcmap": + echo '{}' Step #2 - "srcmap": + PATHS_TO_SCAN=/src Step #2 - "srcmap": + [[ c++ == \g\o ]] Step #2 - "srcmap": ++ find /src -name .git -type d Step #2 - "srcmap": + for DOT_GIT_DIR in $(find $PATHS_TO_SCAN -name ".git" -type d) Step #2 - "srcmap": ++ dirname /src/htslib/.git Step #2 - "srcmap": + GIT_DIR=/src/htslib Step #2 - "srcmap": + cd /src/htslib Step #2 - "srcmap": ++ git config --get remote.origin.url Step #2 - "srcmap": + GIT_URL=https://github.com/samtools/htslib.git Step #2 - "srcmap": ++ git rev-parse HEAD Step #2 - "srcmap": + GIT_REV=8594ac2c11694fff1b1dea341163dbfd3fa212e2 Step #2 - "srcmap": + jq_inplace /tmp/filePSYvuM '."/src/htslib" = { type: "git", url: "https://github.com/samtools/htslib.git", rev: "8594ac2c11694fff1b1dea341163dbfd3fa212e2" }' Step #2 - "srcmap": ++ tempfile Step #2 - "srcmap": + F=/tmp/filexhIgr9 Step #2 - "srcmap": + cat /tmp/filePSYvuM Step #2 - "srcmap": + jq '."/src/htslib" = { type: "git", url: "https://github.com/samtools/htslib.git", rev: "8594ac2c11694fff1b1dea341163dbfd3fa212e2" }' Step #2 - "srcmap": + mv /tmp/filexhIgr9 /tmp/filePSYvuM Step #2 - "srcmap": ++ find /src -name .svn -type d Step #2 - "srcmap": ++ find /src -name .hg -type d Step #2 - "srcmap": + '[' '' '!=' '' ']' Step #2 - "srcmap": + cat /tmp/filePSYvuM Step #2 - "srcmap": + rm /tmp/filePSYvuM Step #2 - "srcmap": { Step #2 - "srcmap": "/src/htslib": { Step #2 - "srcmap": "type": "git", Step #2 - "srcmap": "url": "https://github.com/samtools/htslib.git", Step #2 - "srcmap": "rev": "8594ac2c11694fff1b1dea341163dbfd3fa212e2" Step #2 - "srcmap": } Step #2 - "srcmap": } Finished Step #2 - "srcmap" Starting Step #3 - "compile-libfuzzer-coverage-x86_64" Step #3 - "compile-libfuzzer-coverage-x86_64": Already have image (with digest): gcr.io/cloud-builders/docker Step #3 - "compile-libfuzzer-coverage-x86_64": --------------------------------------------------------------- Step #3 - "compile-libfuzzer-coverage-x86_64": vm.mmap_rnd_bits = 28 Step #3 - "compile-libfuzzer-coverage-x86_64": Compiling libFuzzer to /usr/lib/libFuzzingEngine.a... done. Step #3 - "compile-libfuzzer-coverage-x86_64": --------------------------------------------------------------- Step #3 - "compile-libfuzzer-coverage-x86_64": CC=clang Step #3 - "compile-libfuzzer-coverage-x86_64": CXX=clang++ Step #3 - "compile-libfuzzer-coverage-x86_64": CFLAGS=-O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument Step #3 - "compile-libfuzzer-coverage-x86_64": CXXFLAGS=-O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -stdlib=libc++ Step #3 - "compile-libfuzzer-coverage-x86_64": RUSTFLAGS=--cfg fuzzing -Cdebuginfo=1 -Cforce-frame-pointers -Cinstrument-coverage -C link-arg=-lc++ Step #3 - "compile-libfuzzer-coverage-x86_64": --------------------------------------------------------------- Step #3 - "compile-libfuzzer-coverage-x86_64": + autoconf Step #3 - "compile-libfuzzer-coverage-x86_64": + autoheader Step #3 - "compile-libfuzzer-coverage-x86_64": + ./configure Step #3 - "compile-libfuzzer-coverage-x86_64": checking for gcc... clang Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the C compiler works... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for C compiler default output file name... a.out Step #3 - "compile-libfuzzer-coverage-x86_64": checking for suffix of executables... Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether we are cross compiling... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for suffix of object files... o Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether we are using the GNU C compiler... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether clang accepts -g... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for clang option to accept ISO C89... none needed Step #3 - "compile-libfuzzer-coverage-x86_64": checking for ranlib... ranlib Step #3 - "compile-libfuzzer-coverage-x86_64": checking for grep that handles long lines and -e... /usr/bin/grep Step #3 - "compile-libfuzzer-coverage-x86_64": checking for C compiler warning flags... -Wall Step #3 - "compile-libfuzzer-coverage-x86_64": checking how to run the C preprocessor... clang -E Step #3 - "compile-libfuzzer-coverage-x86_64": checking for egrep... /usr/bin/grep -E Step #3 - "compile-libfuzzer-coverage-x86_64": checking for ANSI C header files... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for sys/types.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for sys/stat.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for stdlib.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for string.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for memory.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for strings.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for inttypes.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for stdint.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for unistd.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether _XOPEN_SOURCE is declared... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether __get_cpuid_max is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether __cpuid_count is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking x86intrin.h usability... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking x86intrin.h presence... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for x86intrin.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt Step #3 - "compile-libfuzzer-coverage-x86_64": checking C compiler flags needed for avx2... -mavx2 -mpopcnt Step #3 - "compile-libfuzzer-coverage-x86_64": checking C compiler flags needed for avx512f... -mavx512f -mpopcnt Step #3 - "compile-libfuzzer-coverage-x86_64": checking for working __builtin_cpu_supports("ssse3")... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for working __attribute__((target("ssse3")))... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for pkg-config... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for special C compiler options needed for large files... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for _FILE_OFFSET_BITS value needed for large files... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking shared library type for unknown-Linux... plain .so Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the linker supports versioned symbols... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -fvisibility=hidden... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for stdlib.h... (cached) yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for unistd.h... (cached) yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for sys/param.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for getpagesize... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for working mmap... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for gmtime_r... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for fsync... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for drand48... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for srand48_deterministic... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for getauxval... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for elf_aux_info... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for posix_memalign... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether fdatasync is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for fdatasync... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for __attribute__((constructor))... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for library containing log... none required Step #3 - "compile-libfuzzer-coverage-x86_64": checking for zlib.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for inflate in -lz... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for library containing recv... none required Step #3 - "compile-libfuzzer-coverage-x86_64": checking for bzlib.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for BZ2_bzBuffToBuffCompress in -lbz2... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for lzma.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for lzma_easy_buffer_encode in -llzma... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether htscodecs files are present... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for libdeflate.h... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for libdeflate_deflate_compress in -ldeflate... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for curl/curl.h... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for curl_easy_pause in -lcurl... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for CCHmac... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking for library containing HMAC... -lcrypto Step #3 - "compile-libfuzzer-coverage-x86_64": checking for fstatat... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for CMSG_LEN... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for epoll... yes (edge triggered) Step #3 - "compile-libfuzzer-coverage-x86_64": checking for sendfile... yes, Linux-style Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether EHOSTDOWN is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether ENONET is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether AI_V4MAPPED is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether AI_ADDRCONFIG is declared... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wextra... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wformat... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wformat=2... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wconversion... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wtrampolines... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wstrict-aliasing... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -fstack-clash-protection... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -fstack-protector-strong... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -fcf-protection=full... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -mbranch-protection=standard... no Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -fno-delete-null-pointer-checks... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wl,-z,noexecstack... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wl,-z,relro... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wl,-z,now... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wl,--as-needed... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking whether the compiler accepts -Wl,-z,nodlopen... yes Step #3 - "compile-libfuzzer-coverage-x86_64": checking for library containing regcomp... none required Step #3 - "compile-libfuzzer-coverage-x86_64": configure: creating ./config.status Step #3 - "compile-libfuzzer-coverage-x86_64": config.status: creating config.mk Step #3 - "compile-libfuzzer-coverage-x86_64": config.status: creating htslib.pc.tmp Step #3 - "compile-libfuzzer-coverage-x86_64": config.status: creating config.h Step #3 - "compile-libfuzzer-coverage-x86_64": config.status: linking htscodecs_bundled.mk to htscodecs.mk Step #3 - "compile-libfuzzer-coverage-x86_64": ++ nproc Step #3 - "compile-libfuzzer-coverage-x86_64": + make -j32 libhts.a test/fuzz/hts_open_fuzzer.o Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o kfunc.o kfunc.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o kstring.o kstring.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o bgzf.o bgzf.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o errmod.o errmod.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o faidx.o faidx.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o header.o header.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hfile.o hfile.c Step #3 - "compile-libfuzzer-coverage-x86_64": echo '#define HTS_VERSION_TEXT "1.22.1-1-g8594ac2"' > version.h Step #3 - "compile-libfuzzer-coverage-x86_64": printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ Step #3 - "compile-libfuzzer-coverage-x86_64": 'clang' \ Step #3 - "compile-libfuzzer-coverage-x86_64": '' \ Step #3 - "compile-libfuzzer-coverage-x86_64": '-Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden' \ Step #3 - "compile-libfuzzer-coverage-x86_64": '-fvisibility=hidden ' \ Step #3 - "compile-libfuzzer-coverage-x86_64": '-llzma -lbz2 -lz -lcurl -lcrypto' > config_vars.h Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hts_os.o hts_os.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o md5.o md5.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o multipart.o multipart.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o probaln.o probaln.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o realn.o realn.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o regidx.o regidx.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o region.o region.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o sam.o sam.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o sam_mods.o sam_mods.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o simd.o simd.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o tbx.o tbx.c Step #3 - "compile-libfuzzer-coverage-x86_64": Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.6.4-ga815cd0" Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o textutils.o textutils.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o vcf.o vcf.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c Step #3 - "compile-libfuzzer-coverage-x86_64": cram/cram_decode.c:2312:31: warning: unused variable 'q_id' [-Wunused-variable] Step #3 - "compile-libfuzzer-coverage-x86_64": 2312 | int qsize=0, nsize=0, q_id=0; Step #3 - "compile-libfuzzer-coverage-x86_64": |  ^~~~ Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -mavx2 -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -mavx512f -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -msse4.1 -mssse3 -mpopcnt -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hfile_libcurl.o hfile_libcurl.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hfile_gcs.o hfile_gcs.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hfile_s3.o hfile_s3.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hfile_s3_write.o hfile_s3_write.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c Step #3 - "compile-libfuzzer-coverage-x86_64": clang -Wall -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -fvisibility=hidden -I. -c -o hts.o hts.c Step #3 - "compile-libfuzzer-coverage-x86_64": 1 warning generated. Step #3 - "compile-libfuzzer-coverage-x86_64": ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o Step #3 - "compile-libfuzzer-coverage-x86_64": ranlib libhts.a Step #3 - "compile-libfuzzer-coverage-x86_64": + clang++ -O1 -fno-omit-frame-pointer -gline-tables-only -Wno-error=incompatible-function-pointer-types -Wno-error=int-conversion -Wno-error=deprecated-declarations -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=unknown-warning-option -Wno-error=vla-cxx-extension -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION -fprofile-instr-generate -fcoverage-mapping -pthread -Wl,--no-as-needed -Wl,-ldl -Wl,-lm -Wno-unused-command-line-argument -stdlib=libc++ -o /workspace/out/libfuzzer-coverage-x86_64/hts_open_fuzzer test/fuzz/hts_open_fuzzer.o -fsanitize=fuzzer libhts.a -lz -lbz2 -llzma -lcurl -lcrypto -lpthread Finished Step #3 - "compile-libfuzzer-coverage-x86_64" Starting Step #4 Step #4: Pulling image: gcr.io/oss-fuzz-base/base-runner Step #4: Using default tag: latest Step #4: latest: Pulling from oss-fuzz-base/base-runner Step #4: b549f31133a9: Already exists Step #4: fbd651eef87f: Already exists Step #4: 1213aebcf1ee: Already exists Step #4: 159bfcba0ec1: Pulling fs layer Step #4: 151d203047ba: Pulling fs layer Step #4: ae91c9e86ee2: Pulling fs layer Step #4: 5dddfb68a37f: Pulling fs layer Step #4: d1987f23a844: Pulling fs layer Step #4: 079afb30a636: Pulling fs layer Step #4: 6e7c8674c91b: Pulling fs layer Step #4: 3e2f40aed1e2: Pulling fs layer Step #4: 05440077cdb5: Pulling fs layer Step #4: ccdf9af96bb5: Pulling fs layer Step #4: c2de5c419b37: Pulling fs layer Step #4: 05e243ea265e: Pulling fs layer Step #4: ad1c0c2bd206: Pulling fs layer Step #4: 08341a55e67c: Pulling fs layer Step #4: a1f8be6052bc: Pulling fs layer Step #4: 1b3eebaf3697: Pulling fs layer Step #4: aa88d2a73e4f: Pulling fs layer Step #4: df87eb8e0601: Pulling fs layer Step #4: f9b6ffc45d89: Pulling fs layer Step #4: 7e085c869f68: Pulling fs layer Step 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complete Step #4: 5dddfb68a37f: Verifying Checksum Step #4: 5dddfb68a37f: Download complete Step #4: 6e7c8674c91b: Verifying Checksum Step #4: 6e7c8674c91b: Download complete Step #4: 3e2f40aed1e2: Verifying Checksum Step #4: 3e2f40aed1e2: Download complete Step #4: 159bfcba0ec1: Pull complete Step #4: 05440077cdb5: Verifying Checksum Step #4: 05440077cdb5: Download complete Step #4: 05e243ea265e: Verifying Checksum Step #4: 05e243ea265e: Download complete Step #4: c2de5c419b37: Verifying Checksum Step #4: c2de5c419b37: Download complete Step #4: ad1c0c2bd206: Verifying Checksum Step #4: ad1c0c2bd206: Download complete Step #4: a1f8be6052bc: Download complete Step #4: 079afb30a636: Verifying Checksum Step #4: 079afb30a636: Download complete Step #4: 151d203047ba: Pull complete Step #4: aa88d2a73e4f: Verifying Checksum Step #4: aa88d2a73e4f: Download complete Step #4: ae91c9e86ee2: Pull complete Step #4: df87eb8e0601: Verifying Checksum Step #4: df87eb8e0601: Download complete Step #4: 938a06431544: Download complete Step #4: 7e085c869f68: Verifying Checksum Step #4: 7e085c869f68: Download complete Step #4: ccdf9af96bb5: Verifying Checksum Step #4: ccdf9af96bb5: Download complete Step #4: 5dddfb68a37f: Pull complete Step #4: 03157d513924: Verifying Checksum Step #4: 03157d513924: Download complete Step #4: 77ecb77cc680: Verifying Checksum Step #4: 77ecb77cc680: Download complete Step #4: d1987f23a844: Pull complete Step #4: 99a8e6749860: Verifying Checksum Step #4: 99a8e6749860: Download complete Step #4: f9b6ffc45d89: Verifying Checksum Step #4: f9b6ffc45d89: Download complete Step #4: 08341a55e67c: Verifying Checksum Step #4: 08341a55e67c: Download complete Step #4: 1b3eebaf3697: Verifying Checksum Step #4: 1b3eebaf3697: Download complete Step #4: 079afb30a636: Pull complete Step #4: 6e7c8674c91b: Pull complete Step #4: 3e2f40aed1e2: Pull complete Step #4: 05440077cdb5: Pull complete Step #4: ccdf9af96bb5: Pull complete Step #4: c2de5c419b37: Pull complete Step #4: 05e243ea265e: Pull complete Step #4: ad1c0c2bd206: Pull complete Step #4: 08341a55e67c: Pull complete Step #4: a1f8be6052bc: Pull complete Step #4: 1b3eebaf3697: Pull complete Step #4: aa88d2a73e4f: Pull complete Step #4: df87eb8e0601: Pull complete Step #4: f9b6ffc45d89: Pull complete Step #4: 7e085c869f68: Pull complete Step #4: 938a06431544: Pull complete Step #4: 99a8e6749860: Pull complete Step #4: 03157d513924: Pull complete Step #4: 77ecb77cc680: Pull complete Step #4: Digest: sha256:cd72d13b77b6e6e5b4eb6fe7bf76f472326f214752dd653fe1fd32f2c58ab1ce Step #4: Status: Downloaded newer image for gcr.io/oss-fuzz-base/base-runner:latest Step #4: gcr.io/oss-fuzz-base/base-runner:latest Finished Step #4 Starting Step #5 Step #5: Already have image (with digest): gcr.io/oss-fuzz-base/base-runner Step #5: Running hts_open_fuzzer Step #5: Error occured while running hts_open_fuzzer: Step #5: Cov returncode: 0, grep returncode: 0 Step #5: INFO: Running with entropic power schedule (0xFF, 100). Step #5: INFO: Seed: 1062374834 Step #5: MERGE-OUTER: 7595 files, 0 in the initial corpus, 0 processed earlier Step #5: MERGE-OUTER: attempt 1 Step #5: INFO: Running with entropic power schedule (0xFF, 100). Step #5: INFO: Seed: 1062411174 Step #5: INFO: -max_len is not provided; libFuzzer will not generate inputs larger than 1048576 bytes Step #5: MERGE-INNER: using the control file '/tmp/libFuzzerTemp.Merge39.txt' Step #5: MERGE-INNER: 7595 total files; 0 processed earlier; will process 7595 files now Step #5: #1 pulse exec/s: 0 rss: 35Mb Step #5: #2 pulse exec/s: 0 rss: 35Mb Step #5: #4 pulse exec/s: 0 rss: 35Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: #8 pulse exec/s: 0 rss: 35Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: #16 pulse exec/s: 0 rss: 37Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: #32 pulse exec/s: 0 rss: 37Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: #64 pulse exec/s: 0 rss: 37Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bcf_hdr_read] Failed to read the header (reading BCF in text mode?) Step #5: [E::bcf_hdr_read] Failed to read the header (reading BCF in text mode?) Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bcf_hdr_read] Failed to read the header (reading BCF in text mode?) Step #5: [E::bcf_hdr_read] Failed to read the header (reading BCF in text mode?) Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Step #5: [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Step #5: #128 pulse exec/s: 0 rss: 38Mb Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " " Step #5: [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Step #5: [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " ÿ" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " ÿ" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " ÿ" Step #5: [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Step #5: [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " (N" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " (N" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " (N" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@" Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: #256 pulse exec/s: 0 rss: 42Mb Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@CÕ" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@CÕ" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@CÕ" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN: " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN: " Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN: " Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " VN(µ/ý" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " VN(µ/ý" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " VN(µ/ý" Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Missing tab at line 2: "¼°" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "¼°" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "¼°" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@ÿÿÿ°" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@ÿÿÿ°" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 2: "@ÿÿÿ°" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "–" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "–" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "–" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 3: "@" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 3: "@" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 3: "@" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "@C" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "@C" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "@C" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xFDi" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xFDi" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::sam_hrecs_error] Missing tab at line 2: "õc" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "õc" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "õc" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xDD\xBE" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xDD\xBE" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 ( ) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 ( ) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 ( ) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 () Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 () Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 () Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 (ÿ) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 (ÿ) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 (ÿ) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##=" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##=" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##=" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##=" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x1A\xA0" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x1A\xA0" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xD7B" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xD7B" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xD7B" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xD7B" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: #512 pulse exec/s: 0 rss: 49Mb Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">\xA9" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">\xA9" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "$#%\\" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "$#%\\" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::crypt4gh_needed] Accessing "data" needs the crypt4gh plug-in. Step #5: It can be found at https://github.com/samtools/htslib-crypt4gh Step #5: You also need to rebuild HTSlib with plug-ins enabled. Step #5: If you have the plug-in, please ensure it can be found on your HTS_PATH. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID: Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHR\r\x02" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHR\r\x02" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with no LN: tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@®" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@®" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@®" Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@®" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Missing tab at line 2: "÷c" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "÷c" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "÷c" Step #5: [W::cram_get_ref] Failed to populate reference "O" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Out of memory Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "ü" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHR" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHR" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [E::fai_build_core] File truncated at line 1 Step #5: [E::refs_load_fai] Failed to open reference file '-' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " Sirect_" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " Sirect_" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " Sirect_" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse1] no SQ lines present in the header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xDB" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: "B>" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xDB" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: "B>" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [W::cram_get_ref] Failed to populate reference "$" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHRO=" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHRO=" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::cram_get_ref] Failed to populate reference ":" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#\x04" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#\x04" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\x9C=<\x12" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\x9C=<\x12" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\x9C=<\x12" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\x9C=<\x12" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#C\x11Rv\x02" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#C\x11Rv\x02" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHROB" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHROB" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [E::sam_hrecs_error] Header line too short at line 1: "@" Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [E::sam_hdr_build_from_sam_file] Invalid header line: must start with @HD/@SQ/@RG/@PG/@CO Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::fai_build3_core] Failed to open the file f7: : Protocol not supported Step #5: [E::refs_load_fai] Failed to open reference file 'f7:' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::fai_build3_core] Failed to open the file &3 : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file '&3' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 (ò*ÿ,-0) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 (ò*ÿ,-0) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 (ò*ÿ,-0) Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::fai_build3_core] Failed to open the file fl : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 'fl' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xF3\xA0\x80\xB4B\t" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xF3\xA0\x80\xB4B\t" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xF3\xA0\x80\xB4B\t" Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##\xF3\xA0\x80\xB4B\t" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::cram_get_ref] Failed to populate reference "‫" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::fai_build3_core] Failed to open the file f0: : Protocol not supported Step #5: [E::refs_load_fai] Failed to open reference file 'f0:' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xEE"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xEE"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xEE"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "³- -256" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "8"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "8"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "8"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_get_ref] Failed to populate reference "E]t\" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bcf_hdr_parse_line] Missing ']' in header line "##E=" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#C>" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##@=' Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xEF"; treated as unmapped Step #5: [E::aux_parse] unrecognized type '>' Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xEF"; treated as unmapped Step #5: [E::aux_parse] unrecognized type '>' Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::fai_build3_core] Failed to open the file /// : Is a directory Step #5: [E::refs_load_fai] Failed to open reference file '///' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::fai_build3_core] Failed to open the file fila : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 'fila ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##@=RO%0a%_.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>RO%0a%_' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID R Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID R Step #5: Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: gs:hÿÿÿÿÿÿ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'gs:hÿÿÿÿÿÿ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xEF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xEF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xEF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POSöIR Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POSöIR Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_error] Missing tab at line 2: "O I* 1:11:1B@f" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "O I* 1:11:1B@f" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "O I* 1:11:1B@f" Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xF6\xCB\xCD\xCF\xCB\xCB\xC8\xC906"...; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xF6\xCB\xCD\xCF\xCB\xCB\xC8\xC906"...; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xF6\xCB\xCD\xCF\xCB\xCB\xC8\xC906"...; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=,**' Step #5: [W::cram_get_ref] Failed to populate reference "¤¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:@7/896:þÿÿ|: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:@7/896:þÿÿ|' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 35 Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 35 Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 35 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] numeric value out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] numeric value out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] numeric value out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build3_core] Failed to open the file file : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 'file' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "1 10" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "1 10" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "1 10" with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 35 Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 35 Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 35 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "_ is:_" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "41"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "41"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "41"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] File truncated at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@:Ta+) %0a­' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%0aO@0ai: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3::O%0O¥0a%_O%0a>%0aO@0ai' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] File truncated at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@:T%0a+)í' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Missing ']' in header line "##J=z_:aA_%0a%8a.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:aA_%0a%8a' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Missing ']' in header line "##J=" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">0>1" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">W>" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">0>1" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">W>" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xFF\xFF\xFF" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xFF\xFF\xFF\xFF>" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">0>1" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">W>" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">0>1" Step #5: [W::bcf_hdr_parse] Could not parse header line: ">W>" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\xFF\xFF\xFF" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: s3:%%: ,~@6/ý7z@ÿ¹r: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:%%: ,~@6/ý7z@ÿ¹r' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQí" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#\\\\\\\\\\\\\\\\\\\\\\\\\\\\DVt\\\\\t" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#\\\\\\\\\\\\\\\\\\\\\\\\\\\\DVt\\\\\t" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=z_:]O8ÍZF_7@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::fai_build_core] File truncated at line 1 Step #5: [E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,‹Í>z_:]O8­¾¥¹_7@oQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::fai_build_core] File truncated at line 4 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@aWWW¤¨¨¨%0a%)0%%a+%0aWWW' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized mate reference name ">7:9"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Unrecognized type B:Z Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ">7:9"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Unrecognized type B:Z Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ">7:9"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Unrecognized type B:Z Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::fai_build_core] File truncated at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@%0a+iíºTO%17014105727a%d0ß' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "”" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: s3:/wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwg: No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 's3:/wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwg' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::process_one_read] Unknown CIGAR op code 9 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:C Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:C Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:C Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xAF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xAF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xAF"; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: s3:b-------------ÒÒ/-------ÒÒ/----ÙA: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:b-------------ÒÒ/-------ÒÒ/----ÙA' Step #5: [W::cram_get_ref] Failed to populate reference "?" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:*daat:ÿ,@::i?&: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*daat:ÿ,@::i?&' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:UR:%0aÿ%_O%0a%0a>/?' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::process_one_read] Unknown CIGAR op code 9 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] ð encodes a CIGAR with 13 operators at the CG tag Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] ð encodes a CIGAR with 13 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] ð encodes a CIGAR with 13 operators at the CG tag Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::process_one_read] CIGAR and query sequence are of different length Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 8224 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8224 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] number outside allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] number outside allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] number outside allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID RE? A Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID RE? A Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] unrecognized type ',' Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] unrecognized type ',' Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] unrecognized type ',' Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 8224 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8224 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::process_one_read] CIGAR and query sequence are of different length Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 15 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 15 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 15 operators at the CG tag Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bgzf_read_block] Invalid BGZF header at offset 35 Step #5: [E::bgzf_read_block] Invalid BGZF header at offset 35 Step #5: [E::bgzf_read_block] Invalid BGZF header at offset 35 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] number outside allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] number outside allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] number outside allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "V"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "V"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "V"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##F=z_:aA_%½0a%0a> %0O%0a#Ã%0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'daTa:aÚ:,>z_:aA_%½0a%0a> %0O%0a#Ã%0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "V"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "4"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "V"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "4"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "V"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "4"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 13 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 13 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 13 operators at the CG tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SN:_ isiAM LN:4294967040" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID÷§EF ALTú¿ Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID÷§EF ALTú¿ Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 18 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 18 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 18 operators at the CG tag Step #5: [E::process_one_read] Unknown CIGAR op code 9 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Header line too short at line 1: "ü" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 18 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 18 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 18 operators at the CG tag Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=z_:aA_%½819199577a!0a> %0O%0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\x9F"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\x9F"; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\x9F"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=z_:O%0a%_O%0A>%d%0?%öa>:O%0aB.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:O%0a%_O%0A>%d%0?%öa>:O%0aB' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] Quality line length too long in ':T%0)½@:T%' at line 5 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@:T%0)½@:T%%0ae%0a+)e’%0ae%0a+)íº­' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::lzma_mem_inflate] LZMA decode failure (error 7) Step #5: [E::lzma_mem_inflate] LZMA decode failure (error 7) Step #5: [E::lzma_mem_inflate] LZMA decode failure (error 7) Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=T0Tº2@>0/w%CRAM ?' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>=%_O%[a00T/>T0Tº2@>0/w%CRAM ?' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SÎ:Æ " Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHRV\t" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHRV\t" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::fai_build_core] File truncated at line 2 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@ [ ,.1ï,2,.ÿ.1' Step #5: [W::cram_get_ref] Failed to populate reference "¤-.0,2-,.1ï,2,.¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:i Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:i Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:i Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:fhttphdr_callb:d-214~2/Ú: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:fhttphdr_callb:d-214~2/Ú' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 768 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 768 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_error] Header line does not start with '@' at line 2: "ï LN:822082515" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: s3:*da: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*da' Step #5: [W::cram_get_ref] Failed to populate reference "›" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:OO%0RiR:d%0a%0a%0a%0a> %0aO%0a.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:OO%0RiR:d%0a%0a%0a%0a> %0aO%0a' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID³ÿ1ý0ððøððð Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID³ÿ1ý0ððøððð Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@S," Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@S," Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@S," Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 1: "@S," Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@SQ' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@SQ' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##=\xFFte-z >|%0ai:sý7zÿ0aiR:O%0a%_O%0a>%0a0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z >|%0ai:sý7zÿ0aiR:O%0a%_O%0a>%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: s3://////////////////////////////////////////sss: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3://////////////////////////////////////////sss' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '„' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "„" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '„' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "„" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID PEF ALT QUAL FILT»­¹EF ALT QUAL FILT» Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID PEF ALT QUAL FILT»­¹EF ALT QUAL FILT» Step #5: Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REmat=VCF Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REmat=VCF Step #5: Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 150 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO ',' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QU' is not defined in the header Step #5: [W::vcf_parse_info] INFO ',' is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO ',' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '„' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '„' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :258 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::inflate_gzip_block] Inflate operation failed: incorrect data check Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Inflate operation failed: incorrect data check Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::inflate_gzip_block] Inflate operation failed: incorrect data check Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 51 Step #5: [E::bgzf_read_block] Failed to read BGZF header at offset 51 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bgzf_read_block] Invalid BGZF block length at offset 0 Step #5: [E::bgzf_read_block] Invalid BGZF block length at offset 0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##or&I" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##or&I" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :116 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :1693 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at @:0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'áö' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "áö" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'áö' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "áö" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER '[' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '[' is not defined in the header Step #5: [E::bcf_hdr_parse_line] Missing ']' in header line "##FILTER=" Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER '[' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<##fmat>dddddddVCF" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=dddddddVCF" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=,Number=1,Type=String,Description=\"Dummy\">"' Step #5: [W::bcf_hrec_check] Invalid tag name: "pg0_ù" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO 'pg0_ù>' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'pg0_ù>' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=,Number=1,Type=String,Description=\"Dummy\">"' Step #5: [W::bcf_hrec_check] Invalid tag name: "pg0_ù" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO 'pg0_ù>' at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised key: Bÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Bÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Bÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key áè Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key áè Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key áè Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_byte_array_len_decode_init] Malformed byte_array_len header stream Step #5: [E::cram_byte_array_len_decode_init] Malformed byte_array_len header stream Step #5: [E::cram_byte_array_len_decode_init] Malformed byte_array_len header stream Step #5: Malformed const header stream Step #5: Malformed const header stream Step #5: Malformed const header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B1 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B1 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B1 Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SÎ:Æ " Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key F4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key € Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key âN Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ,ÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key º Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key F4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key € Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key âN Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ,ÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key º Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key F4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key € Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key âN Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ,ÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key º Step #5: Malformed varint header stream Step #5: Malformed varint header stream Step #5: Malformed varint header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xdelta header stream Step #5: Malformed xdelta header stream Step #5: Malformed xdelta header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [E::cram_byte_array_stop_decode_init] The byte_array_stop codec only supports BYTE_ARRAYs Step #5: [E::cram_byte_array_stop_decode_init] The byte_array_stop codec only supports BYTE_ARRAYs Step #5: [E::cram_byte_array_stop_decode_init] The byte_array_stop codec only supports BYTE_ARRAYs Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: Malformed xrle header stream Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: Malformed xrle header stream Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: Malformed xrle header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: Malformed xrle header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xpack header stream Step #5: Malformed const header stream Step #5: Malformed const header stream Step #5: Malformed const header stream Step #5: Malformed varint header stream Step #5: Malformed varint header stream Step #5: Malformed varint header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [E::cram_byte_array_stop_decode_init] Malformed byte_array_stop header stream Step #5: [E::cram_byte_array_stop_decode_init] Malformed byte_array_stop header stream Step #5: [E::cram_byte_array_stop_decode_init] Malformed byte_array_stop header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line " " with multiple LN: tag with different values. Step #5: [W::cram_decode_compression_header] Unrecognised key: ä Step #5: [W::cram_decode_compression_header] Unrecognised key: ä Step #5: [W::cram_decode_compression_header] Unrecognised key: ä Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB_RICE Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB_RICE Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB_RICE Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type ? Step #5: [E::cram_decoder_init] Unimplemented codec of type ? Step #5: [E::cram_decoder_init] Unimplemented codec of type ? Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: Malformed xrle header stream Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: Malformed xrle header stream Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: Malformed xrle header stream Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "*?"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "ó ‡" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "*?"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 () Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 1 () Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :2070400 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "6,,,,,,,,,,460"; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 17 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "6,,,,,,,,,,460"; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 17 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "6,,,,,,,,,,460"; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 17 operators at the CG tag Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key æ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key : Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key æ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key : Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key æ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key : Step #5: [W::sam_parse1] unrecognized mate reference name "\xC9\xC9\xC8)\xC9\xC9\xC9\xC9\xC9\"...; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "\xC9\xC9\xC8)\xC9\xC9\xC9\xC9\xC9\"...; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "\xC9\xC9\xC8)\xC9\xC9\xC9\xC9\xC9\"...; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build3_core] Failed to open FASTQ index data:,@Ilqe0aWWWWWWWWeW¤¨¨¨%0a%)0Ú%0a+©¨¨%0a%)0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@Ilqe0aWWWWWWWWeW¤¨¨¨%0a%)0Ú%0a+©¨¨%0a%)0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_beta_decode_init] Malformed beta header stream Step #5: Malformed xdelta header stream Step #5: [E::cram_beta_decode_init] Malformed beta header stream Step #5: Malformed xdelta header stream Step #5: [E::cram_beta_decode_init] Malformed beta header stream Step #5: Malformed xdelta header stream Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '32769' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '32769' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at @:0 Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "`"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "`"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "`"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '32767' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::vcf_parse_info] INFO '#' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "#" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '32767' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::vcf_parse_info] INFO '#' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "#" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ' Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B¿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÷ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 0S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ' Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B¿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÷ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 0S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ' Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B¿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÷ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 0S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '##fileformat=VCF' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '##fileformat=VCF' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: s3:f:d@Ÿ:f?iR~:/&/²RŒÿÿÿÿÿÿÿÿÿet:ÿ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:d@Ÿ:f?iR~:/&/²RŒÿÿÿÿÿÿÿÿÿet:ÿ' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::sam_hrecs_error] Missing tab at line 1: "é" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '%' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '…(…ÇEF' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ALT' is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '%' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '…(…ÇEF' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ALT' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::vcf_hdr_read] No sample line Step #5: [E::vcf_hdr_read] No sample line Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QULTER INFO Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QULTER INFO Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:bme--,ÒÒÒÒ---------11111111---------------------/--': Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:bme--,ÒÒÒÒ---------11111111---------------------/--'' Step #5: [W::cram_get_ref] Failed to populate reference "?" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: s3:f:d@Ÿ:f?iR~:/&+²R:sredYe::f:d@Ÿ:f?iR~:/&/²R:sredir: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:d@Ÿ:f?iR~:/&+²R:sredYe::f:d@Ÿ:f?iR~:/&/²R:sredir' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'fa' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '.' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "." Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not parse the position 'ò' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'fa' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '.' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "." Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at fa:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'qR' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ó#' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'qR' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ó#' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::cram_encode_aux] Missing @RG header for RG "@CO" Step #5: [W::cram_encode_aux] Missing @RG header for RG "ž" Step #5: [W::cram_encode_aux] Missing @RG header for RG "," Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 34 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 34 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 34 operators at the CG tag Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8224 Step #5: [E::process_one_read] Mapped read with position <= 0 is disallowed Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8224 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8224 Step #5: [E::process_one_read] Mapped read with position <= 0 is disallowed Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8224 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at @:0 Step #5: s3:*da:,t@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*da:,t@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "›" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :10352035200 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_alloc4] Duplicate FORMAT tag at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '¶¶¶¶LTER' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'RA' is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '¶¶¶¶LTER' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'RA' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'Ä' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ä" Step #5: [W::vcf_parse_info] INFO 'Ä!' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ä!" Step #5: [W::vcf_parse_info] INFO '-' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "-" Step #5: [W::vcf_parse_info] INFO 'Ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ÿ" Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'Ä' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ä" Step #5: [W::vcf_parse_info] INFO 'Ä!' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ä!" Step #5: [W::vcf_parse_info] INFO '-' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "-" Step #5: [W::vcf_parse_info] INFO 'Ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ÿ" Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '9223372034283418426' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '9223372034283418426' is too large Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '18446744068496267386' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '18446744068496267386' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not parse the position '36893488:4482461117' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not parse the position '36893488:4482461117' Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " LÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿN:!¨#cpÅTypeècoÿ{{{{{{{{{{{{" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " LÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿN:!¨#cpÅTypeècoÿ{{{{{{{{{{{{" Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " LÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿN:!¨#cpÅTypeècoÿ{{{{{{{{{{{{" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " LÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿN:!¨#cpÅTypeècoÿ{{{{{{{{{{{{" Step #5: [E::bgzf_read_block] Invalid BGZF header at offset 58 Step #5: [E::bgzf_read_block] Invalid BGZF header at offset 58 Step #5: [E::bgzf_read_block] Invalid BGZF header at offset 58 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '18446744063282715910' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '18446744063282715910' is too large Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at @:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :1716409479 Step #5: BYTE_ARRAYs not supported by this codec Step #5: Malformed xpack header stream Step #5: BYTE_ARRAYs not supported by this codec Step #5: Malformed xpack header stream Step #5: BYTE_ARRAYs not supported by this codec Step #5: Malformed xpack header stream Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '36893488144812461117' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '36893488144812461117' is too large Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 88 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 7 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key PP Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key -- Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 7P Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 88 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 7 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key PP Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key -- Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 7P Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 88 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 7 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key PP Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key -- Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 7P Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_refs_from_targets_array] Duplicate entry "" in target list Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_refs_from_targets_array] Duplicate entry "" in target list Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_refs_from_targets_array] Duplicate entry "" in target list Step #5: [E::sam_hrecs_refs_from_targets_array] Duplicate entry "" in target list Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '18446744063283517930' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '18446744063283517930' is too large Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: BYTE_ARRAYs not supported by this codec Step #5: BYTE_ARRAYs not supported by this codec Step #5: BYTE_ARRAYs not supported by this codec Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID RE; ALT QUAL FILT,R IT Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID RE; ALT QUAL FILT,R IT Step #5: Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '600002000166600103556' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '600002000166600103556' is too large Step #5: [W::cram_get_ref] Failed to populate reference ":aSQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '457360066933775026490' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '457360066933775026490' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '....' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '....' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at ....:0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :34887607492394 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##IN(OVCF" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##IN(OVCF" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::fai_build_core] File truncated at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@%0a+iíºTO%170141183460469231731687303715884105727a%d0ß' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :17440126714846 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::vcf_parse_format_empty1] FORMAT column with no sample columns starting at :0 Step #5: [E::bcf_write] Broken VCF record, the number of columns at :0 does not match the number of samples (0 vs 1) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::vcf_parse_format_empty1] FORMAT column with no sample columns starting at :0 Step #5: [E::bcf_write] Broken VCF record, the number of columns at :0 does not match the number of samples (0 vs 1) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :43739106746195 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::vcf_parse_info] INFO 'ß@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ß@" Step #5: [W::vcf_parse_info] INFO 'F' is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::vcf_parse_info] INFO 'ß@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ß@" Step #5: [W::vcf_parse_info] INFO 'F' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:O%0ó ?' has no sequence at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:(>a,>R:a%_O%0a>/%ó ?O%0á%_O%0a>/%ó:,>R:O%0ó ?' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] Quality line length too long in 'úHlp' at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@úHlp%0a+ata:,@úHlp%0a-.CRAM'À' Step #5: [W::cram_get_ref] Failed to populate reference "¤-.0,2-,.1ï,2,.¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::fai_build_core] File truncated at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@úHlp%0a1y,0%%%%%%%Desc%%%vvvvvvv.01' Step #5: [W::cram_get_ref] Failed to populate reference "¤:.¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " SÎ:!vvv@sQ SÎ:!vvvvvv " Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '_:Ožžžžž.1,.0RGBZC' is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '_:Ožžžžž.1,.0RGBZC' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '_:Ožžžžž.1,.0RGBZC' is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '_:Ožžžžž.1,.0RGBZC' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_add_sample_len] Duplicated sample name 'RE' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_add_sample_len] Duplicated sample name 'RE' Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'è' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "è" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'è' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "è" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'FIL' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'FIL' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "^"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:I array Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "^"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:I array Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "^"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:I array Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::bgzf_read_init] Cannot decompress legacy RAZF format Step #5: [E::razf_info] To decompress this file, use the following command: Step #5: gunzip FILE Step #5: This will likely produce a "trailing garbage ignored" message, which can Step #5: usually be safely ignored. Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::fai_build_core] Quality length longer than sequence in 'Ilp,@Ilp' at line 7 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0a%)0%%0a+%0aWWW¤¨¨¨%0a%)0%%0a+©ª­Åda' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:fh>;»>?0>ã4;m?0U>;>>?4m?0U>;>~2)Ú: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:fh>;»>?0>ã4;m?0U>;>>?4m?0U>;>~2)Ú' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ó' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ó" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ó' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ó" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_aux] Unsupported SAM aux type 'd' Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_get_ref] Failed to populate reference "‰‰‰‰‰‰" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 15 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 15 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 15 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "âAN9 AN:-36##fió »" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '00000200016660106550526103556' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Position value '00000200016660106550526103556' is too large Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "1"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "1"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "â ŒKSQü÷ű¬;ontó ±)gLM: AN:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: Malformed varint header stream Step #5: Malformed varint header stream Step #5: Malformed varint header stream Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHROMN:\xFF\xFF\xFF\xFF(\xFF#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_hdr_parse] Could not parse header line: "#CHROMN:\xFF\xFF\xFF\xFF(\xFF#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ó ‚U' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'Æ' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ó ‚U' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'Æ' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ó ‚' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'Æ' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ó ‚' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'Æ' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'è' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "è" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'è' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "è" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '1' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '1' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "\xD2"; treated as unmapped Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "\xD2"; treated as unmapped Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized mate reference name "\xD2"; treated as unmapped Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "&ÿ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "‌/SQü÷Åÿÿÿÿÿÿÿÿ±ó €«Ä±¬;ontó ±igLM:2:&IAN9 AN:-36##, " Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::vcf_parse_info] INFO 'ßÀ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ßÀ" Step #5: [W::vcf_parse_info] INFO 'À' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "À" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ÿþ' is not defined in the header Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::vcf_parse_info] INFO 'ßÀ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ßÀ" Step #5: [W::vcf_parse_info] INFO 'À' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "À" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ÿ>Cf flag 1024 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read ÿ>Cf flag 1024 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GZ' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read  flag 65024 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 65024 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:ü@PG Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:ü@PG Step #5: [W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:ü@PG Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿÿÿÿÿÿÿÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿÿÿÿÿÿÿÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::vcf_parse_format_dict2] Invalid FORMAT tag name '.' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿÿÿÿÿÿÿÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿÿÿÿÿÿÿÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::vcf_parse_format_dict2] Invalid FORMAT tag name '.' at :0 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line with no SN: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Invalid character '[' in 'GT' FORMAT field at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Invalid character '[' in 'GT' FORMAT field at :0 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:I Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:I Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:I Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '%T' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "%T" Step #5: [W::vcf_parse_format_dict2] FORMAT 'F' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'FloGT;' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FloGT;" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '%T' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "%T" Step #5: [W::vcf_parse_format_dict2] FORMAT 'F' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'FloGT;' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FloGT;" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Malformed varint header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Malformed varint header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Malformed varint header stream Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: NN Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: NN Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: NN Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿC Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿC Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿC Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Malformed varint header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Malformed varint header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Malformed varint header stream Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'O' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'B' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'O' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'B' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '$g–' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '…' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'CO' is not defined in the header Step #5: [W::vcf_parse_info] INFO ' ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: " " Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '$g–' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '…' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'CO' is not defined in the header Step #5: [W::vcf_parse_info] INFO ' ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: " " Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::cram_decode_compression_header] Unrecognised key: NN Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: NN Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: NN Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::cram_encode_aux] Unsupported SAM aux type 'd' Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'H' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1                ' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'H' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1                ' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at H:0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:bme/---------------11111111111111111111111111111-----------------/--': Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:bme/---------------11111111111111111111111111111-----------------/--'' Step #5: [W::cram_get_ref] Failed to populate reference "?" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xpack header stream Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xpack header stream Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xpack header stream Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xdelta header stream Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xdelta header stream Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xdelta header stream Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "d"; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "d"; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "d"; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xpack header stream Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xpack header stream Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: [W::cram_decode_compression_header] Codec for key IN defined more than once Step #5: Malformed xpack header stream Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFOb=R:O%0á%_O%0a%_O%0a>/%ó ÿþ¼?aO@^aiO%0aL%_O%0a> 0a%_O%0a@?aO.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>R:O%0á%_O%0a%_O%0a>/%ó ÿþ¼?aO@^aiO%0aL%_O%0a> 0a%_O%0a@?aO' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 2: " LN: " Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:f%%%%%%%%%%0%%%%%%%%%%%%%%%%%%ØØï0%%%%%%%%%%%%%%%%%%ØØ@:/: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f%%%%%%%%%%0%%%%%%%%%%%%%%%%%%ØØï0%%%%%%%%%%%%%%%%%%ØØ@:/' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: s3:f:d@G:f?iR//²:R&~ù/²:R&~..:s3:f:d@œ:f?3:f/²:R&~ûøøøø......: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:d@G:f?iR//²:R&~ù/²:R&~..:s3:f:d@œ:f?3:f/²:R&~ûøøøø......' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER 'Q  ,,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'Q  ,,' is not defined in the header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=" Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER 'Q  ,,' at :0 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POSßÿ+=Óï Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POSßÿ+=Óï Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POSßÿ+=Óï Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POSßÿ+=Óï Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read ÿ flag 768 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'FIL' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '+/v/2`2` [' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'FIL' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 28 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 28 Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:fhttphdr_callb:d/&;+{’’’Ð^redirecUR:s3:f:d/&;+;’’’A’’~2/Ú: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:fhttphdr_callb:d/&;+{’’’Ð^redirecUR:s3:f:d/&;+;’’’A’’~2/Ú' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾,@::iÒ>' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:O%0á%_O%9223372036854775808a%_O%0%0a%_O%0a>O%2147483648a@?aO' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::fai_build_core] Quality line length too long in '))))))))T%' at line 5 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@))))))))T%%0a ûÿÖþe%0a+) ÿae%127a@:T%%0a ûÿÖþe%0a+) ÿ+)íº,0' Step #5: [W::cram_get_ref] Failed to populate reference "//:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT2' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '9' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "9" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT2' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '9' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "9" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read @@@@ flag 65024 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read @@@@ flag 65024 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [E::aux_parse] unrecognized type '\xBE' Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::aux_parse] unrecognized type '\xBE' Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::aux_parse] unrecognized type '\xBE' Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x7F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4034539577: Invalid CONTIG id 892403255 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: Invalid FILTER type 12 (unknown) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: Invalid INFO id 10473 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4034539577 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x7F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4034539577: Invalid CONTIG id 892403255 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: Invalid FILTER type 12 (unknown) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4034539577: Invalid INFO id 10473 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4034539577 - shared section malformed or too short Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QUAL FILTER INFO FOR INFO FORMAT , Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QUAL FILTER INFO FOR INFO FORMAT , Step #5: Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 100663297: Invalid CONTIG id 823 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):100663297: Invalid ID type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):100663297 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 100663297: Invalid CONTIG id 823 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):100663297: Invalid ID type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):100663297 - shared section malformed or too short Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "‌/XSQü÷ű󠀫CRAMontó ±igLM:2:&IAO9 AN:-36##,õxÓÓÓÓÓÓ',,ÿÿ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x7F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4034539577: Invalid CONTIG id 892403511 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4034539577 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x7F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4034539577: Invalid CONTIG id 892403511 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4034539577 - shared section malformed or too short Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'T' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO 'INFO' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'FO¦MA' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FO¦MA" Step #5: [E::vcf_parse_format_max3] Incorrect number of FORMAT fields at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'T' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key N Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key N Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key N Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 100663297: Invalid CONTIG id 311 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):100663297: Invalid ID type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):100663297 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 100663297: Invalid CONTIG id 311 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):100663297: Invalid ID type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):100663297 - shared section malformed or too short Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ÿÿEE flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read ÿÿEE flag 0 Step #5: [E::cram_encode_aux] Unsupported SAM aux type '' Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 26 Step #5: [E::fai_build_core] Format error, unexpected character at line 10 Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:OO%0a>%0a0aiR:2O%1aLN:Ol%0a%0a>%0aO@0aÍa%0a>%0aO@0aiRiR:d%0a%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER ' ' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER ' ' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER ' ' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER ' ' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:OO%0a>%0a0aiR:2O%1aLN:Ol%0a%0a>%0aO@0aÍa%0a>%0AO@0aiRiR:d%0;a%0a0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:OO%0a>%0a0aiR:2O%1aLN:Ol%0a%0a>%0aO@0aÍa%0a>%0AO@0aiRiR:d%0;a%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 1376126471: Invalid CONTIG id 101058048 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1376126471: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1376126471: No REF allele Step #5: [E::bcf_record_check] Bad BCF record at (unknown):1376126471 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 1376126471: Invalid CONTIG id 101058048 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1376126471: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1376126471: No REF allele Step #5: [E::bcf_record_check] Bad BCF record at (unknown):1376126471 - shared section malformed or too short Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] B aux field type not followed by ',' Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] B aux field type not followed by ',' Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 1: Invalid CONTIG id 25899 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1: Invalid INFO id 1 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):1 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 1: Invalid CONTIG id 25899 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):1: Invalid INFO id 1 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):1 - shared section malformed or too short Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "M\x01)" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x99nCRAM\x04\x02 \xDC 244/\xFF\xFF\xFF\x9FP \x0Et\\-!" Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QUALþ¹ILT@SQ ER INFO Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "M\x01)" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x99nCRAM\x04\x02 \xDC 244/\xFF\xFF\xFF\x9FP \x0Et\\-!" Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QUALþ¹ILT@SQ ER INFO Step #5: [E::bcf_hdr_read] Failed to read BCF header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Missing tab at line 2: "RN HHH" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "RN HHH" Step #5: [E::sam_hrecs_error] Missing tab at line 2: "RN HHH" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :258 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '80445423ÿÿAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FILfTER' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'INFOo' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '80445423ÿÿAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FILfTER' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'INFOo' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:f:d@Ÿ:f?¡­²ÅÅ¡’šm_peVCFvSN::ÿGGGGGGGGGGGGGGGG::GGG::::2ó €­.'1,ÿÿÿÿÿÿ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:d@Ÿ:f?¡­²ÅÅ¡’šm_peVCFvSN::ÿGGGGGGGGGGGGGGGG::GGG::::2ó €­.'1,ÿÿÿÿÿÿ' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '[' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=:`2ð¡¡¡¡ÊÊʲº12121212121212121212121212121212129: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*daat:ÿ%@::i?ÿÿÿÿÿÿÞ2?5>:`2ð¡¡¡¡ÊÊʲº12121212121212121212121212121212129' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:O%0á%_O%0a%_O%0a>/%ó ?aO@^aiO%0aL%_O%0a> 1a%_O%0%0a%_O%0a>O%0a@?aO.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>R:O%0á%_O%0a%_O%0a>/%ó ?aO@^aiO%0aL%_O%0a> 1a%_O%0%0a%_O%0a>O%0a@?aO' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '[' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:O%0á%_O%0a%_O%0a>/%ó ÞaO@^aiO%0aL%_O%0a> 1a%_O%0%0a%_O%0a>O%0a@?aO.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>R:O%0á%_O%0a%_O%0a>/%ó ÞaO@^aiO%0aL%_O%0a> 1a%_O%0%0a%_O%0a>O%0a@?aO' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'cont' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '%T' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "%T" Step #5: [W::vcf_parse_format_dict2] FORMAT 'NT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿA»ö' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿA»ö" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'cont' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '%T' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "%T" Step #5: [W::vcf_parse_format_dict2] FORMAT 'NT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿA»ö' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿA»ö" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:C array Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:C array Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read %ö flag 8318 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "@S" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read %ö flag 8318 Step #5: [E::bam_aux_next] Corrupted aux data for read %ö flag 8318 Step #5: [E::bam_aux_next] Corrupted aux data for read %ö flag 8318 Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 0: Invalid CONTIG id -202 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):0: Invalid ID type 2 (int (16 bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):0: Invalid REF/ALT type 15 (unknown) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):0 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 0: Invalid CONTIG id -202 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):0: Invalid ID type 2 (int (16 bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):0: Invalid REF/ALT type 15 (unknown) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):0 - shared section malformed or too short Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO= Step #5: Step #5: MS: 0 ; base unit: 0000000000000000000000000000000000000000 Step #5: 0x42,0x41,0x4d,0x1,0x0,0x0,0x0,0x0,0x1,0x0,0x0,0x0,0x2,0x0,0x0,0x0,0x40,0x53,0x51,0x9,0x2f,0xfd,0x4f,0x0,0x0,0x0,0x0,0x0,0x0,0x0,0x40,0x67,0x28,0x32,0x2,0x42,0x2c,0x46,0x9,0x0,0x7e,0x20,0x0,0x0,0x0,0x0,0x0,0x0,0x0,0x0,0xff,0xfb,0xdb,0x23,0x9a,0x66,0x61,0x69,0x25,0x5a,0xf6,0xff,0x2c,0x2c,0x2c,0x2c,0xb6,0x0,0x0,0xa,0x9,0x9,0x9,0x31,0x9,0x9,0x30,0x53,0x9,0x9,0x9,0x9,0x9,0xa,0x9,0x9,0x9,0x79,0x70,0x65,0x3d,0x2c,0x2c,0x2c,0x0,0x0,0x0,0x0,0x91,0x42,0x48,0x0,0xff,0xed,0xff,0xef,0x0, Step #5: BAM\001\000\000\000\000\001\000\000\000\002\000\000\000@SQ\011/\375O\000\000\000\000\000\000\000@g(2\002B,F\011\000~ \000\000\000\000\000\000\000\000\377\373\333#\232fai%Z\366\377,,,,\266\000\000\012\011\011\0111\011\0110S\011\011\011\011\011\012\011\011\011ype=,,,\000\000\000\000\221BH\000\377\355\377\357\000 Step #5: artifact_prefix='./'; Test unit written to ./oom-259d39337a1d992163837e7e8eaa6ceae4b8e79f Step #5: Base64: QkFNAQAAAAABAAAAAgAAAEBTUQkv/U8AAAAAAAAAQGcoMgJCLEYJAH4gAAAAAAAAAAD/+9sjmmZhaSVa9v8sLCwstgAACgkJCTEJCTBTCQkJCQkKCQkJeXBlPSwsLAAAAACRQkgA/+3/7wA= Step #5: SUMMARY: libFuzzer: out-of-memory Step #5: MERGE-OUTER: attempt 2 Step #5: INFO: Running with entropic power schedule (0xFF, 100). Step #5: INFO: Seed: 1069444746 Step #5: INFO: -max_len is not provided; libFuzzer will not generate inputs larger than 1048576 bytes Step #5: MERGE-INNER: using the control file '/tmp/libFuzzerTemp.Merge39.txt' Step #5: MERGE-INNER: '/corpus/hts_open_fuzzer/259d39337a1d992163837e7e8eaa6ceae4b8e79f' caused a failure at the previous merge step Step #5: MERGE-INNER: 7595 total files; 4047 processed earlier; will process 3548 files now Step #5: [E::hts_hopen] Failed to open file data Step #5: #1 pulse exec/s: 0 rss: 36Mb Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 4 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 22 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 4 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 22 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 4 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 22 operators at the CG tag Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: #2 pulse exec/s: 0 rss: 37Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: #4 pulse exec/s: 0 rss: 39Mb Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x7F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 978203705: Invalid CONTIG id 904265527 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):978203705: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):978203705: Invalid REF/ALT type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):978203705 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x7F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 978203705: Invalid CONTIG id 904265527 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):978203705: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):978203705: Invalid REF/ALT type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):978203705 - shared section malformed or too short Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:s Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:s Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "8:"; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:s Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: #8 pulse exec/s: 0 rss: 40Mb Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_get] Corrupted aux data for read ‘d flag 8318 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_get] Corrupted aux data for read ‘d flag 8318 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "Û" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_get] Corrupted aux data for read ‘d flag 8318 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '.AT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ".AT" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '.AT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ".AT" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER '8<=8,$3' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER '8<=8,$3' at :0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18adai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18i"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18adai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18i"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18adai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18i"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_get] Corrupted aux data for read ‘d flag 8318 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_get] Corrupted aux data for read ‘d flag 8318 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_get] Corrupted aux data for read ‘d flag 8318 Step #5: #16 pulse exec/s: 0 rss: 41Mb Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 0s Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key t4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key PA Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 3c Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ob Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key dC Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key AM Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ? Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key RA Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key „ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 00 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key !> Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 0s Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key t4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key PA Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 3c Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ob Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key dC Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key AM Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ? Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key RA Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key „ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 00 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key !> Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 0s Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key t4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key PA Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 3c Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ob Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key dC Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key AM Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ? Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key RA Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key „ Step #5: #32 pulse exec/s: 0 rss: 106Mb Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "ï" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4029742386: Invalid CONTIG id -13028553 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4029742386: Invalid ID type 2 (int (16 bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4029742386: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4029742386: Invalid FILTER type 0 (null) Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4029742386: Invalid CONTIG id -13028553 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4029742386: Invalid ID type 2 (int (16 bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4029742386: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4029742386: Invalid FILTER type 0 (null) Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ## flag 65535 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " " Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::bam_aux_next] Corrupted aux data for read ## flag 65535 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:SSSSSSSSSSSSSSSS:aO%1aLN:OO%@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:SSSSSSSSSSSSSSSS:aO%1aLN:OO%@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQí" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ffff flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read ffff flag 0 Step #5: [E::cram_encode_aux] Unsupported SAM aux type '™' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO ',,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FILTER)INF' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FILTER)INF" Step #5: [W::vcf_parse_info] INFO ',,' is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO ',,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER ',,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'FILTER)INF' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER ',,' is not defined in the header Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=" Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER ',,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FILTER' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'INFOMRMÿÿÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "INFOMRMÿÿÿ" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FILTER' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'INFOMRMÿÿÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "INFOMRMÿÿÿ" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Invalid BAM binary header Step #5: #64 pulse exec/s: 0 rss: 107Mb Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ÿ flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::cram_put_bam_seq] CIGAR query length 268431408 for read "ÿ" is too long Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'T' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'QUALMAT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_empty1] FORMAT column with no sample columns starting at :0 Step #5: [E::bcf_write] Broken VCF record, the number of columns at :0 does not match the number of samples (0 vs 1) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'T' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'QUALMAT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTS' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTS' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4278190081: Invalid CONTIG id 13631283 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4278190081: Invalid ID type 1 (int (8-bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4278190081: Invalid REF/ALT type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4278190081 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4278190081: Invalid CONTIG id 13631283 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4278190081: Invalid ID type 1 (int (8-bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4278190081: Invalid REF/ALT type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4278190081 - shared section malformed or too short Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ":\xAD\xA8\x05"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "3[\x80\x02"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "S9M::"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ":\xAD\xA8\x05"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "3[\x80\x02"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "S9M::"; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "2" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ":\xAD\xA8\x05"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "3[\x80\x02"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "S9M::"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " INFOSN: LN:::⊠UR:data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0%p;xá… calc\x165359185a%)p,@Ilp%0aWWW¤¨¨¨%00%%0a+%0aWWW" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " INFOSN: LN:::⊠UR:data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0%p;xá… calc\x165359185a%)p,@Ilp%0aWWW¤¨¨¨%00%%0a+%0aWWW" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " INFOSN: LN:::⊠UR:data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0%p;xá… calc\x165359185a%)p,@Ilp%0aWWW¤¨¨¨%00%%0a+%0aWWW" Step #5: s3:f:d@Ÿ:f?iR~:/&/:f:d@Ÿ:f?hR~:/ó ¯&/:f:d@Ÿ:f?iR~:/&/:f:d@ó ?iR~:ó ™/&/²â€ƒR1srediir: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:d@Ÿ:f?iR~:/&/:f:d@Ÿ:f?hR~:/ó ¯&/:f:d@Ÿ:f?iR~:/&/:f:d@ó ?iR~:ó ™/&/²â€ƒR1srediir' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ":\xAD\xA8\x05"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "a4di"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "S9M:0:6"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "a4di"; treated as unmapped Step #5: [E::parse_cigar] CIGAR length invalid at position 2 (#1`=<) Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ":\xAD\xA8\x05"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "a4di"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "S9M:0:6"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "a4di"; treated as unmapped Step #5: [E::parse_cigar] CIGAR length invalid at position 2 (#1`=<) Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_get_ref] Failed to populate reference "2" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ":\xAD\xA8\x05"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "a4di"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "S9M:0:6"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "a4di"; treated as unmapped Step #5: [E::parse_cigar] CIGAR length invalid at position 2 (#1`=<) Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_parse1] unrecognized mate reference name "4"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] unrecognized mate reference name "4"; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_parse1] unrecognized mate reference name "4"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '@' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER 'ilefor1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '0' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at @:0 Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " INFOSN: LN:::⊠UR:data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0%p;xá… calc\x165359185a%)p,@Ilp%0aWWW¤¨¨¨%00%%0a+%0aWWW" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " INFOSN: LN:::⊠UR:data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0%p;xá… calc\x165359185a%)p,@Ilp%0aWWW¤¨¨¨%00%%0a+%0aWWW" Step #5: [E::sam_hrecs_error] Malformed key:value pair at line 1: " INFOSN: LN:::⊠UR:data:,@Ilp,@Ilp%0aWWW¤¨¨¨%0%p;xá… calc\x165359185a%)p,@Ilp%0aWWW¤¨¨¨%00%%0a+%0aWWW" Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 66 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 66 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 66 operators at the CG tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_error] Header line does not start with '@' at line 1: "€" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [E::cram_encode_aux] Unsupported SAM aux type 'd' Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] unrecognized type '\0' Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] unrecognized type '\0' Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "‌/SQü÷Ågggggggggggggggggggggggggggggggggggggggggggggg0000 AN:-" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 413090613 for read "" is too long Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC32\xC3\xC3##\xEFolrfeim" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 1: Invalid CONTIG id 0 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):1 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC32\xC3\xC3##\xEFolrfeim" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 1: Invalid CONTIG id 0 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):1 - shared section malformed or too short Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] File truncated at line 2 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@úHlp%0 a' Step #5: [W::cram_get_ref] Failed to populate reference "¤¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTS' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTS' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_read1] CIGAR and query sequence lengths differ for Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_read1] CIGAR and query sequence lengths differ for Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_error] Header line does not start with '@' at line 2: "ï LN:4252349907" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:%%: ,@8?ÿÿ(N:: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:%%: ,@8?ÿÿ(N:' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQíhhhhhððððð/////ÿ: ,hhhhhhhhððððð/////////////////" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8Ç' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "8Ç" Step #5: [E::vcf_parse] Could not parse the position '+¨¨-->Èÿ' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8Ç' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "8Ç" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ºGT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ºGT" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '…2' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "…2" Step #5: [W::vcf_parse_format_dict2] FORMAT '»' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "»" Step #5: [W::vcf_parse_format_dict2] FORMAT '@SQ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@SQ" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ºGT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ºGT" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '…2' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "…2" Step #5: [W::vcf_parse_format_dict2] FORMAT '»' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "»" Step #5: [W::vcf_parse_format_dict2] FORMAT '@SQ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@SQ" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::fai_build_core] Quality line length too long in 'úHlp' at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@úHlp%0a+ata:,@úHlp%0a-.02,.01, :SN:zÌÑÏÓ2,-.1,2, ,01-.1,2,‹.Ù1' Step #5: [W::cram_get_ref] Failed to populate reference "¤-.0,2-(µ/ý,.1ï,2,.¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::fai_build3_core] Failed to open FASTA index data:a:,>R:O%0á%_O%0a%_O%0a>/%ó ?aOdata:a:,@^aiO%0aL%_O%0a> 1a%_O%0%0a%_O%0a>O%0a@?aO.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>R:O%0á%_O%0a%_O%0a>/%ó ?aOdata:a:,@^aiO%0aL%_O%0a> 1a%_O%0%0a%_O%0a>O%0a@?aO' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'ID' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "ID" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'RT' at ID:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at ID:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'ID' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "ID" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'RT' at ID:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at ID:0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at ID:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=RÁ°ÚÏÚ €O%0_Oa%0%a>/%ó ?aOdata:a:,@^aiO0%aL%_%0> 1Oaa%_O~0%0_¶a%0%Oa>O%0a@?Ÿ¬.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>RÁ°ÚÏÚ €O%0_Oa%0%a>/%ó ?aOdata:a:,@^aiO0%aL%_%0> 1Oaa%_O~0%0_¶a%0%Oa>O%0a@?Ÿ¬' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'Q'ALTENF' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '!$' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '?' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'Q'ALTENF' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '!$' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '?' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=>%0a0ahRO%0a>%0a0ahRO%0a>%0a0ahRO%0a>%0a0ahR0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>>%0a0ahRO%0a>%0a0ahRO%0a>%0a0ahRO%0a>%0a0ahR0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 30 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 30 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 30 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: ".(8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '.(8<' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: ".(8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '.(8<' at :0 Step #5: [E::cram_huffman_decode_init] BYTE_ARRAYs not supported by this codec Step #5: [E::cram_huffman_decode_init] BYTE_ARRAYs not supported by this codec Step #5: [E::cram_huffman_decode_init] BYTE_ARRAYs not supported by this codec Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "‌/SQü÷ű󠀫ı¬;ontó ±igLM:2:&IAN9 AN:-36##, ‡,,ÏÓ,,,,, , " Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:O%0a%_OOa%_O%0}A>$d%0a%0a%0d%0a%0d%0A>%?%0a%0,>za%0a%0d%0a%0d0a%0,,>z_:O%0a%_O' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##" Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'REF' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ALT' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig 'Fv35,-4,-23,-24,-223372N-1,-g24' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##contig=" Step #5: [E::vcf_parse] Could not add dummy header for contig 'Fv35,-4,-23,-24,-223372N-1,-g24' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##" Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'REF' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ALT' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTS' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTS' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::cram_subexp_decode_init] This codec only supports INT encodings Step #5: [E::cram_subexp_decode_init] This codec only supports INT encodings Step #5: [E::cram_subexp_decode_init] This codec only supports INT encodings Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'YYYYYYa128+INFO1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '.' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '?' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'Ë' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER ':5' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER ':' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'YY' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'YYYYYYa128+INFO1' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '.' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '?' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'Ë' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER ':5' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER ':' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'YY' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=' in a FASTQ file, error at line 7 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@Ilp%0aWWW¤¨¨¨%0a%)0%%0a+©ª­Ådata:Ó@:IlL%0aWWWUWWW%0a%0a>)-ÿÿÿÿ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:O%0a%_OO%0A>%d%0a%0,>z_:O%0a%_O%0A>%d%0a%%_O%0A>%d%0a%0a%0A>%d%0a%0ÿa>ÿ.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aa:aÚ:,>z_:O%0a%_OO%0A>%d%0a%0,>z_:O%0a%_O%0A>%d%0a%%_O%0A>%d%0a%0a%0A>%d%0a%0ÿa>ÿ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read HHHH flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::cram_encode_aux] Unterminated HH:H tag for read "HHHH" Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: AM Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB_RICE Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: AM Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB_RICE Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: AM Step #5: [E::cram_decoder_init] Unimplemented codec of type GOLOMB_RICE Step #5: [E::fai_build_core] The last entry '%%0:.data:,@ú¯lta' has no sequence at line 6 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@úHlp%0a#WW¤¨¨¨%0a%)0%%0a+©ª­Åd===================================ata%0aWWWUWWW%0a@%%0:.data:,@ú¯lta' Step #5: [W::cram_get_ref] Failed to populate reference "¤¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::fai_build_core] File truncated at line 2 Step #5: [E::refs_load_fai] Failed to open reference file 'data:CRfai¦¦¦¦¦¦¦¦¦ÿ¦RO%0a%>0:::C:R%:f_aid_%:¦¦¦a:,>:_:O%0%:,2.'2,.02,.01,-.1,2-,(.1ï,2,.02,.01,-&1,2,-TD.1,-.1 ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ÿ flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "¥ï" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read ÿ flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read ÿ flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read ÿ flag 128 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'zf.' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '@©ÿ©P' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@©ÿ©P" Step #5: [E::vcf_parse_format_dict2] Invalid FORMAT tag name '.' at zf.:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'zf.' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '@©ÿ©P' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@©ÿ©P" Step #5: [E::vcf_parse_format_dict2] Invalid FORMAT tag name '.' at zf.:0 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:ta:a:,>R:O%0a%_O%0a>.%0ÿaO@ËaiO%0aLN:O%0a>%_øøøøRÿ:O%0a%_O%0a>BO%5a%_O%0a>.%0aO@1aiO%0aLN:O.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a*:,>R:ta:a:,>R:O%0a%_O%0a>.%0ÿaO@ËaiO%0aLN:O%0a>%_øøøøRÿ:O%0a%_O%0a>BO%5a%_O%0a>.%0aO@1aiO%0aLN:O' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_read_slice] Unexpected block of type EXTERNAL Step #5: [E::cram_read_slice] Unexpected block of type EXTERNAL Step #5: [E::cram_read_slice] Unexpected block of type EXTERNAL Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_hdr_read] Truncated BAM header Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at :0 Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: Malformed xpack header stream Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'hZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x07"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x07"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x07"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'F' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '=' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "=" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at F:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '/' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "/" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::vcf_parse_format_check7] Number of columns at F:0 does not match the number of samples (0 vs 11) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'F' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '=' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "=" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at F:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '/' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "/" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at F:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::vcf_parse_format_check7] Number of columns at F:0 does not match the number of samples (0 vs 11) Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: AM Step #5: [W::cram_decode_compression_header] Unrecognised key: Hƒ Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: AM Step #5: [W::cram_decode_compression_header] Unrecognised key: Hƒ Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: AM Step #5: [W::cram_decode_compression_header] Unrecognised key: Hƒ Step #5: [E::cram_decoder_init] Unimplemented codec of type NULL Step #5: Malformed xrle header stream Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0S"; treated as unmapped Step #5: [E::cram_generate_reference] Cannot build reference with unsorted data Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:aA_1ÿÿÿÿÿÿäO%Ш%RR>_&O_%0a>%%a#%0a>_O%0a> ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 762054922: Invalid CONTIG id 866778901 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: Invalid FILTER type 14 (unknown) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: Invalid INFO id -256 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):762054922 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 762054922: Invalid CONTIG id 866778901 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: Invalid FILTER type 14 (unknown) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):762054922: Invalid INFO id -256 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):762054922 - shared section malformed or too short Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] Incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18adai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18i"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18adai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18i"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18adai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "d\x18i"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'Zè' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Zè" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '1000G' is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_empty1] FORMAT column with no sample columns starting at :0 Step #5: [E::bcf_write] Broken VCF record, the number of columns at :0 does not match the number of samples (0 vs 1) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'Zè' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Zè" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=À`:AÒ>&-&&>->&&,,*,,,da:,tva_listaÿ:@::™?256i&`:AÒ>&]&: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*da:,taÅ¿ÅÅfÀÓ5i&:&>À`:AÒ>&-&&>->&&,,*,,,da:,tva_listaÿ:@::™?256i&`:AÒ>&]&' Step #5: [W::cram_get_ref] Failed to populate reference "›" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::cram_encode_aux] Unsupported SAM aux type '' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:OO%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@ %0aiR8sý7zÿ0aiR:O%0a%_O%0a>%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ID' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLR' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLR" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'ID' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLR' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLR" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 42 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 42 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 42 operators at the CG tag Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 939393024: Invalid CONTIG id -3145932 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):939393024: Invalid ID type 2 (int (16 bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):939393024: No REF allele Step #5: [E::bcf_record_check] Bad BCF record at (unknown):939393024 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 939393024: Invalid CONTIG id -3145932 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):939393024: Invalid ID type 2 (int (16 bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):939393024: No REF allele Step #5: [E::bcf_record_check] Bad BCF record at (unknown):939393024 - shared section malformed or too short Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'cont' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '%T' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "%T" Step #5: [W::vcf_parse_format_dict2] FORMAT 'NT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '-m' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "-m" Step #5: [W::vcf_parse_format_dict2] FORMAT 'FMemX' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Ä25604861AT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ä25604861AT" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿA»ö' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿA»ö" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'cont' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '%T' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "%T" Step #5: [W::vcf_parse_format_dict2] FORMAT 'NT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '-m' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "-m" Step #5: [W::vcf_parse_format_dict2] FORMAT 'FMemX' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Ä25604861AT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Ä25604861AT" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿA»ö' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿA»ö" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::vcf_parse] Position value '18446744073709551615' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :2147483649 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '[' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at :0 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3#3884470rm" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 2583691232: Invalid CONTIG id -7371692 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):2583691232: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):2583691232: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):2583691232: Invalid FILTER type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):2583691232 - individuals section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3#3884470rm" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 2583691232: Invalid CONTIG id -7371692 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):2583691232: Invalid ID type 0 (null) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):2583691232: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):2583691232: Invalid FILTER type 0 (null) Step #5: [E::bcf_record_check] Bad BCF record at (unknown):2583691232 - individuals section malformed or too short Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO= Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: .S Step #5: [W::cram_decode_compression_header] Unrecognised key: B$ Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: UN Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: .S Step #5: [W::cram_decode_compression_header] Unrecognised key: B$ Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: T+ Step #5: [W::cram_decode_compression_header] Unrecognised key: +P Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: UN Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: .S Step #5: [W::cram_decode_compression_header] Unrecognised key: B$ Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: $U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: 'H Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: :. Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: .S Step #5: [W::cram_decode_compression_header] Unrecognised key: B$ Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: $U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: 'H Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: :. Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: .S Step #5: [W::cram_decode_compression_header] Unrecognised key: B$ Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %W Step #5: [W::cram_decode_compression_header] Unrecognised key: $U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: D% Step #5: [W::cram_decode_compression_header] Unrecognised key: 'H Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: :. Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: N Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=\xFF\xFF\xFF\xFF\xFF\xFF\xFF\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5"' Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xFF\xFF\xFF\xFF\xFF\xFF\xFF\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5\xB5"' Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: !$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $G Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T. Step #5: [W::cram_decode_compression_header] Unrecognised key: 7T Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "% Step #5: [W::cram_decode_compression_header] Unrecognised key: ." Step #5: [W::cram_decode_compression_header] Unrecognised key: %. Step #5: [W::cram_decode_compression_header] Unrecognised key: .W Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .% Step #5: [W::cram_decode_compression_header] Unrecognised key: $. Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: B7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: B7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: T7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: !$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $G Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T. Step #5: [W::cram_decode_compression_header] Unrecognised key: 7T Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "% Step #5: [W::cram_decode_compression_header] Unrecognised key: ." Step #5: [W::cram_decode_compression_header] Unrecognised key: %. Step #5: [W::cram_decode_compression_header] Unrecognised key: .W Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .% Step #5: [W::cram_decode_compression_header] Unrecognised key: $. Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: B7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: B7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: T7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: !$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $G Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T. Step #5: [W::cram_decode_compression_header] Unrecognised key: 7T Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "% Step #5: [W::cram_decode_compression_header] Unrecognised key: ." Step #5: [W::cram_decode_compression_header] Unrecognised key: %. Step #5: [W::cram_decode_compression_header] Unrecognised key: .W Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .. Step #5: [W::cram_decode_compression_header] Unrecognised key: W. Step #5: [W::cram_decode_compression_header] Unrecognised key: .% Step #5: [W::cram_decode_compression_header] Unrecognised key: $. Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: B7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: B7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7> Step #5: [W::cram_decode_compression_header] Unrecognised key: T7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: G7 Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿÿÿÿÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿÿÿÿÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿÿÿÿÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿÿÿÿÿ" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 65024 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::cram_put_bam_seq] CIGAR query length 238960176 for read "" is too long Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO ',,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FIINFO' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'FORMAT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 84 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 84 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 84 operators at the CG tag Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 9 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 9 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 92 Step #5: [E::fai_build3_core] Failed to open FASTA index data:aÚ:,>z_:a%_0ad%O>:ataARf_O:1O%0aLN:O%0a>%_O%0a>ÿÿÿÿÿL1¸2žÚ0a>%0aO@0aiRiR:d%0a%0a> %0aiR:sý7zÿ0aiR:O%0a%_O%0a>%0a0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:a%_0ad%O>:ataARf_O:1O%0aLN:O%0a>%_O%0a>ÿÿÿÿÿL1¸2žÚ0a>%0aO@0aiRiR:d%0a%0a> %0aiR:sý7zÿ0aiR:O%0a%_O%0a>%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '2r22' is not defined in the header Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::vcf_parse_format_check7] Number of columns at :0 does not match the number of samples (2 vs 3) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '2r22' is not defined in the header Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 9 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 9 Step #5: [E::process_one_read] CIGAR and query sequence are of different length Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [E::sam_parse1] invalid QUAL character Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=g24' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##contig=g24>"' Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not add dummy header for contig '>g24' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO= Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: !$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $G Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .V Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .V Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .V Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: ( Step #5: [W::cram_decode_compression_header] Unrecognised key: $( Step #5: [W::cram_decode_compression_header] Unrecognised key: ( Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: TF Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: !$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $G Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: G! Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .V Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .V Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .V Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: .: Step #5: [W::cram_decode_compression_header] Unrecognised key: N. Step #5: [W::cram_decode_compression_header] Unrecognised key: ( Step #5: [W::cram_decode_compression_header] Unrecognised key: $( Step #5: [W::cram_decode_compression_header] Unrecognised key: ( Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: TF Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: %> Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< =VCF" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< =VCF" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< =VCF" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< 2\x02\r\r\r\r\rD2Z\r\rM\r" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< =VCF" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< =VCF" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< =VCF" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=< 2\x02\r\r\r\r\rD2Z\r\rM\r" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 1408 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read flag 1408 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 1408 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 1408 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 1408 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read flag 1408 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 1408 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 1408 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] unrecognized type '\t' Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] unrecognized type '\t' Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=Pv' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##contig=Pv>"' Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not add dummy header for contig '>Pv' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT.' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::cram_put_bam_seq] CIGAR query length 268435440 for read "ù" is too long Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##conmemtig=" Step #5: [E::vcf_parse] Could not add dummy header for contig '#`¨¨-1,-128U.ICR4035,-24,-g23' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::vcf_parse_filter] FILTER '+' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'È€' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "È€" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: gs:@>%N:0a%0a>%ÿÿ>_Oè!0a>Nib29%ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ4#ƒI0Nib294#ƒI0Nib2: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'gs:@>%N:0a%0a>%ÿÿ>_Oè!0a>Nib29%ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ4#ƒI0Nib294#ƒI0Nib2' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:a%_0ad%O>:ataARf_3O:1O%0aLN:O%0a>%_O%0a¾ÿÿÿÿÿL1H0ÿÿ %0a%0a>%0aiRT:saiR:O%0aL1H0ÿÿ %0a%0a> %0R:2:sý7zÿ0aiR0%O:a%_O%0a>%0a0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:a%_0ad%O>:ataARf_3O:1O%0aLN:O%0a>%_O%0a¾ÿÿÿÿÿL1H0ÿÿ %0a%0a>%0aiRT:saiR:O%0aL1H0ÿÿ %0a%0a> %0R:2:sý7zÿ0aiR0%O:a%_O%0a>%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] unrecognized reference name "262163k"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ","; treated as unmapped Step #5: [E::aux_parse] numeric value out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] unrecognized reference name "262163k"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ","; treated as unmapped Step #5: [E::aux_parse] numeric value out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##iidx#ef#`0\t0" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##idx#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##iidx#ef#`0\t0" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##idx#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:fhttphd: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:fhttphd' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'hZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "hZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '8<' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'F' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'Ä' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ğğ¬ѿA' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'I1NFO' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'Ä!' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ß+@' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'F' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'Ä' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ğğ¬ѿA' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'I1NFO' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT '.ZᾂP©zÿÿ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ".ZᾂP©zÿÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Z" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GÔ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "GÔ" Step #5: [W::vcf_parse_format_dict2] FORMAT '^Gß' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "^Gß" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT '.ZᾂP©zÿÿ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ".ZᾂP©zÿÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Z" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GÔ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "GÔ" Step #5: [W::vcf_parse_format_dict2] FORMAT '^Gß' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "^Gß" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at z:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO 'F,#,†,,,' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'F,#,†,,,' is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO 'F,#,†,,,' at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " " Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 8447 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::bam_aux_next] Corrupted aux data for read  flag 8447 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::cram_encode_aux] Unsupported SAM aux type 'd' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: FT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: T" Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: T" Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [E::cram_decoder_init] Unimplemented codec of type ? Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: FT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: T" Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: T" Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [E::cram_decoder_init] Unimplemented codec of type ? Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: T% Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: TU Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: FT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: MT Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: T" Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: T" Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [E::cram_decoder_init] Unimplemented codec of type ? Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=->&&ÿÿ%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%ÿfqi,,da:,tva_listaÿ:@::™6512i3:%Ù&&bf#````ei&&>=;À,,,,,9(,~33>-: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*da&>->&&ÿÿ%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%ÿfqi,,da:,tva_listaÿ:@::™6512i3:%Ù&&bf#````ei&&>=;À,,,,,9(,~33>-' Step #5: [W::cram_get_ref] Failed to populate reference "›" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::fai_build_core] Quality line length too long in 'úHlp' at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@úHlp%0a+ata:,@úHlp%0a-.02,.01, :ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ`ÿÿÿÿSN:,-.,,-12.1,2, ,01-.1,2,‹..1' Step #5: [W::cram_get_ref] Failed to populate reference "¤-.0,2-,.1ï,2,.¨" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QUAl FILTER INFO Step #5: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: Step #5: #CHROM POS ID REF ALT QUAl FILTER INFO Step #5: Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%dA%4___________-______W__________    _______VCFaaaeaaaaaaaaaa: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:c:d@redIirt_?z-Ëcodnte·ÿÿÿÿÿ/faiažž--ÒÒÒÒÒÒÒÂÒµÉÒÒı¶D=VCFm"ï¼z_:O%-1a%_i_O%0a%_OO%0A>%dA%4___________-______W__________    _______VCFaaaeaaaaaaaaaa' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 40 Step #5: [E::fai_build_core] Different line length in sequence '%$*%0,>zaa' at line 13 Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A%0d%0A>%$%2a%0,>zaa%0d%0%0a%01a0%0a%01a%0%0d0a%0,,>z_:O%0a%_O' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse] Contig '##I' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "^"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "^"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "^"; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "0"; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_filter] FILTER 'È€INFO' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'L' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: [E::cram_external_decode_init] Malformed external header stream Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'C' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "C" Step #5: [W::vcf_parse_filter] FILTER '¥LFIRENFTL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'IO' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'FOR(µ/ýMAT' at C:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FOR(µ/ýMAT" Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'AL' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '##IN»,O=ˆ] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid contig name: "##IN»" Step #5: [E::vcf_parse] Could not add dummy header for contig '##IN»,O=ˆ2' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##contig=2>"' Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not add dummy header for contig '>2' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##I^Q\tF05385" Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'P©ÿÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GÔ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "GÔ" Step #5: [W::vcf_parse_format_dict2] FORMAT '^GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "^GT" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at z:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: gs:@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'gs:@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=ongi,I=ongi,I=ongi,I=ongi,I=z_:OO%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aiO%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aiRiR:d%0a%0a> %0aiR8sý7RiR:d%0a%0a> %0aiR8sý7zÿ0aiR:O%0a%_O%0a>%0a0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:OO%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aiO%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aiRiR:d%0a%0a> %0aiR8sý7RiR:d%0a%0a> %0aiR8sý7zÿ0aiR:O%0a%_O%0a>%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::cram_read_slice] Slice does not include any data blocks Step #5: [E::cram_read_slice] Slice does not include any data blocks Step #5: [E::cram_read_slice] Slice does not include any data blocks Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=/w% ?' has no sequence at line 3 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>=ûUdatUR:data:a:,>R:U>,%-0%0R:data:a,>R:O%0á%$O%,>R:U>,%-0%0R:data:a,>R:O%0á%$O%Ùž%_O%0añ/%ó:,>R:O%0á%_O0a>/   %ó ?O%0á%_O%0a>/%ó:%_&%a>/w% ?' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [E::vcf_parse] Could not add dummy header for contig 'eger,ype=Integer,ID=8<' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [E::vcf_parse] Could not add dummy header for contig 'eger,ype=Integer,ID=8<' Step #5: [E::cram_get_ref] No reference found for id 87044865 Step #5: [E::cram_decode_slice] Unable to fetch reference unknown:8-14877 Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_get_ref] No reference found for id 87044865 Step #5: [E::cram_decode_slice] Unable to fetch reference unknown:8-14877 Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_get_ref] No reference found for id 87044865 Step #5: [E::cram_decode_slice] Unable to fetch reference unknown:8-14877 Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [E::cram_next_slice] Failure to decode slice Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "1Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "1Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [E::fai_build_core] The last entry 'SQ' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "1Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3##\xEFileform" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3##\xEFileform" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse] Contig '##I' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '##I-4,=-2-231,-128U.-128U.ICRcontL-4,--2g24,#2\553¨¨¨¨¨5,-]A' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%d%,>z_:O%O1a%___O%0aD_OO%0A>%d%%0_____________?__________N:ˆ(¨:ÿÿ&&&& : Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:d@rIdIirt_Xz-Ëcodnte·€ÿO%-1žÚ___aÒÒÒÒÒÒÒÒÒÂÒµÒÒÒı¶D=VCFm"ï¼Ú##I%0A>%d%,>z_:O%O1a%___O%0aD_OO%0A>%d%%0_____________?__________N:ˆ(¨:ÿÿ&&&& ' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUALî' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FIR)IN' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FIR)IN" Step #5: [W::vcf_parse_info] INFO 'LT' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'F' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'LI' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'F#ype' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "F#ype" Step #5: [W::vcf_parse_info] INFO '?' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "?" Step #5: [W::vcf_parse_info] INFO ',,ð' is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse_info] Could not add dummy header for INFO ',,ð' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUALî' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FIR)IN' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "FIR)IN" Step #5: [W::vcf_parse_info] INFO 'LT' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'F' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=R:O%0ê' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=2["26873#037>@V]A' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##contig=2[\"26873#037>@V]A>"' Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not add dummy header for contig '>2["26873#037>@V]A' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##FORMAT=,Number=1,Type=String,Description=\"Dummy\">" Step #5: [E::vcf_parse_format_dict2] Could not add dummy header for FORMAT ',taÅ¿ÅÅfÀÓ5i&&>' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'QUAL' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FIL' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'QUAL' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:aA_0ad%O>:ataARf_OO%0a%0a>_&O%170141183460469231731687303715884105729a>%N:0a%0a>%ÿÿ %0a%1a> %0O%0a#%0a>_O%0a>%1r@SO%1%~-t0%0aiR:sa%0a#%0a>_O%0a+%1r@SOO%0a>%1r@SO%1%~-t0a%65535a> %0aiR:.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:aA_0ad%O>:ataARf_OO%0a%0a>_&O%170141183460469231731687303715884105729a>%N:0a%0a>%ÿÿ %0a%1a> %0O%0a#%0a>_O%0a>%1r@SO%1%~-t0%0aiR:sa%0a#%0a>_O%0a+%1r@SOO%0a>%1r@SO%1%~-t0a%65535a> %0aiR:' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO="tSU LN:ÿSN:ÍÁ¤Ý"" Step #5: [W::known_stderr] SAM file corrupted by embedded bwa error/log message Step #5: [W::known_stderr] Use `bwa mem -o file.sam ...` or `bwa sampe -f file.sam ...` instead of `bwa ... > file.sam` Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "1Dz11."; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "1Dz11."; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "1Dz11."; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'h(' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "h(" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '*' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "*" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at *:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '2' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "2" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_filter] FILTER 'Ïøö' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'è' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "è" Step #5: [E::bcf_write] Broken VCF record, the number of columns at :0 does not match the number of samples (0 vs 1) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xAF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xAF"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\xAF"; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '/àP' is not defined in the header Step #5: [W::vcf_parse_info] INFO '©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'CZA' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Æ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Æ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÅÅ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÅÅ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÅÅÅÊÅLR' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÅÅÅÊÅLR" Step #5: [E::vcf_parse_format_check7] Number of columns at :0 does not match the number of samples (6 vs 7) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '/àP' is not defined in the header Step #5: [W::vcf_parse_info] INFO '©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'CZA' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Æ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Æ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÅÅ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÅÅ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÅÅÅÊÅLR' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÅÅÅÊÅLR" Step #5: [E::vcf_parse_format_check7] Number of columns at :0 does not match the number of samples (6 vs 7) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'BAM' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "BAM" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ã$:ãããÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ã$:ãããÿ" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'BAM' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "BAM" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ã$:ãããÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ã$:ãããÿ" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at BAM:0 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] incomplete aux field Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "2<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '2<' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "2<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '2<' at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3##\xEFileform" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4294901569: Invalid CONTIG id 1480870149 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid ID type 1 (int (8-bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid FILTER type 13 (unknown) Step #5: [W::bcf_record_check_err] Bad BCF record at (unknown):4294901569: Invalid FORMAT id 50529027 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4294901569 - individuals section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3##\xEFileform" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4294901569: Invalid CONTIG id 1480870149 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid ID type 1 (int (8-bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid FILTER type 13 (unknown) Step #5: [W::bcf_record_check_err] Bad BCF record at (unknown):4294901569: Invalid FORMAT id 50529027 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4294901569 - individuals section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3##\xEFileform" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4294901569: Invalid CONTIG id 1480909317 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid ID type 1 (int (8-bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid FILTER type 10 (unknown) Step #5: [W::bcf_record_check_err] Bad BCF record at (unknown):4294901569: Invalid FORMAT id 50529027 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4294901569 - individuals section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "F\xC3\xC3\xC3\xC3##\xEFileform" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4294901569: Invalid CONTIG id 1480909317 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid ID type 1 (int (8-bit)) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4294901569: Invalid FILTER type 10 (unknown) Step #5: [W::bcf_record_check_err] Bad BCF record at (unknown):4294901569: Invalid FORMAT id 50529027 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4294901569 - individuals section malformed or too short Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27D112"; treated as unmapped Step #5: s3:fhttphdr_callb:d/&;+{’’’Ðÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’^rer_callb:d/&;+{’’’Ðÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’^redirecUR:s3:f:d/&;ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’’,-01615ÿÿÿr_direcUR:s3:f:d/&;ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’’,-01615ÿÿÿr_ca÷r: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:fhttphdr_callb:d/&;+{’’’Ðÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’^rer_callb:d/&;+{’’’Ðÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’^redirecUR:s3:f:d/&;ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’’,-01615ÿÿÿr_direcUR:s3:f:d/&;ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ+;’’’;A’’,-01615ÿÿÿr_ca÷r' Step #5: [W::cram_get_ref] Failed to populate reference "Š;" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 25 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 34 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 43 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 52 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 61 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 78 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 87 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 102 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 118 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 140 Step #5: [E::fai_build3_core] Failed to open FASTA index data:aÚ:,>z_:OO%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aiO%1aLN:O%/a%0a>%0aO@0aÍa%0a>%0aO@0aiRiR:d%0a%0a> %0aiR8sý7RiR:d%0a%0a> %0aiR8sý7zÿ0aiR:O%0a%_O%0a>%0a0.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:OO%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aiO%1aLN:O%/a%0a>%0aO@0aÍa%0a>%0aO@0aiRiR:d%0a%0a> %0aiR8sý7RiR:d%0a%0a> %0aiR8sý7zÿ0aiR:O%0a%_O%0a>%0a0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '"""",i,,,ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿûÿÿÿÿ/,,ýee' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:OO%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aÍa%0a>%0aO@0aiO%1aLN:O%/a%0a>%0aO@0aÍa%0a>%1aO@0aiRiR:d%0a%0a> %327' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'PddddddddAS@ùQ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "PddddddddAS@ùQ" Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '/' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'PddddddddAS@ùQ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "PddddddddAS@ùQ" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at z:0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=:_:O%0cccccccccc¦¦~¦¦ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ289611MÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ0%0a%0a>:%:¦¦¦#a:,a%\\\\\\\\\˜\0000¦a:,>:_:' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::sam_hrecs_update_hashes] Header includes @RG line with no ID: tag Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Duplicate entry "ûÀ¬®öINF¨ßŽ†Å›\‘N"" in sam header Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig ',1' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "23<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '23<' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "23<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '23<' at :0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "Ïÿ¹ÿÿ&&&/›//,,,,,,,,’’’’’;;;;;_:ÿÿÿÿaO%_O%0&a>%5B¸ýþaO@9a¡R³:0ŸO%;1920VCFvÿÿÿ0B¸ýþaO@1ai41-,-&$&&,ü2<:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: gs:: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'gs:' Step #5: [W::cram_get_ref] Failed to populate reference " GN:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value too large at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::vcf_parse_format_fill5] Couldn't read GT data: value too large at :0 Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::bgzf_read_block] Failed to read BGZF block data at offset 0 expected 238 bytes; hread returned 236 Step #5: [E::bgzf_read_block] Failed to read BGZF block data at offset 0 expected 238 bytes; hread returned 236 Step #5: [E::bgzf_read_block] Failed to read BGZF block data at offset 0 expected 238 bytes; hread returned 236 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER 'T=] Step #5: [0] Step #5: [E::vcf_parse_filter] Could not add dummy header for FILTER 'T=z--36-€ÿÿÿÿÿ" Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::bgzf_read_block] EOF marker is absent. The input may be truncated Step #5: [W::bgzf_read_block] EOF marker is absent. The input may be truncated Step #5: [W::bgzf_read_block] EOF marker is absent. The input may be truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 25728 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bgzf_read_block] EOF marker is absent. The input may be truncated Step #5: [W::bgzf_read_block] EOF marker is absent. The input may be truncated Step #5: [W::bgzf_read_block] EOF marker is absent. The input may be truncated Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%5B¸ýþaO@9a¡R³:0ŸO%;1920VCFvÿÿÿ0B¸ýþaO@1ai41-,-&$&&,ü2<:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<##fileformat=VCF#2\xE2-1u" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::vcf_parse_filter] FILTER 'È€INFO' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FORMAT' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig ']' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "]" Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO 'L' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:aA_0ad%O>:ataARf_OO%0a' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'P©ÿÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ZÿÿÿÿÿÿÔ^' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ZÿÿÿÿÿÿÔ^" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Gä?' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Gä?" Step #5: [E::vcf_parse_format_fill5] Invalid character '.' in 'GT' FORMAT field at z:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'P©ÿÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ZÿÿÿÿÿÿÔ^' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ZÿÿÿÿÿÿÔ^" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Gä?' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Gä?" Step #5: [E::vcf_parse_format_fill5] Invalid character '.' in 'GT' FORMAT field at z:0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'ööööööööööööööööööööîöööööööööööööööööööööööööööööööööööö' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "ööööööööööööööööööööîöööööööööööööööööööööööööööööööööööö" Step #5: [E::vcf_parse] Position value '44444444444444444444444444444444444444444444444444444444444444444444444444' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'ööööööööööööööööööööîöööööööööööööööööööööööööööööööööööö' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "ööööööööööööööööööööîöööööööööööööööööööööööööööööööööööö" Step #5: [E::vcf_parse] Position value '44444444444444444444444444444444444444444444444444444444444444444444444444' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=z_:aA_0ad%O>:ataARf_OO%0a%0a>_&O%0a>%N:0a%0a>%ÿÿ %0a%0a> %0O%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r1%~-t0a%0a> %0ait:sa%0a#%0a>_O%0a>%1r@%aiR?sa%0a#%0a>_iR:sa%0a#%0a>_a> %0aiR:sa%0a#%0a>@O%0a>%1r@SO%1%t~-0a%0O%0a' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\x1227Dz11."; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\x1227Dz11."; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "\x1227Dz11."; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##contig=<##fileformat=VCF#2\xE2-1u" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0N' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0N" Step #5: [W::vcf_parse] Contig ']' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "]" Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_filter] FILTER 'È€INFO' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'L' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_2"b29:::ÿÿÿÿÿÿÿÿÿÿVC4b294_#4:924#ƒI0Nm@2b2¿|¶Ï±–Í9Tÿÿÿÿÿÿÿÿÿÿÿÿ#ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ"ormat=VCFfffÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿfffteger,Iÿ::::::' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: s3:f:ðd@Ÿ:f?iR~:/&+²R:alINFOc`&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&懜ž“œÛÖxcaf?iR~:/&+²R:alINFOc`懜ž“œÛ‡œž“œÛ×xcalc)%#wBÅI:: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:ðd@Ÿ:f?iR~:/&+²R:alINFOc`&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&懜ž“œÛÖxcaf?iR~:/&+²R:alINFOc`懜ž“œÛ‡œž“œÛ×xcalc)%#wBÅI:' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿÿÌ'' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿÌ'" Step #5: [W::vcf_parse_format_dict2] FORMAT '©PÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "©PÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "G" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿÿÌ'' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿÌ'" Step #5: [W::vcf_parse_format_dict2] FORMAT '©PÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "©PÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "G" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at z:0 Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::hts_close] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 8447 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " " Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 203033834 for read "" is too long Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:#f:f:dÑÑÑÑÑÑÑÑÑSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSÁSSÑÑÑÑÑÑÑR:s3:#f:f:dÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑ1ÑÑÃ/..SSSSSSSSSSSSSSSSSSSSSÁSSÑÑÑÑÑÑÑR:s3:#f:f:dÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑ1ÑÑÃ/..'ÑÑ240,%1: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:#f:f:dÑÑÑÑÑÑÑÑÑSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSÁSSÑÑÑÑÑÑÑR:s3:#f:f:dÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑ1ÑÑÃ/..SSSSSSSSSSSSSSSSSSSSSÁSSÑÑÑÑÑÑÑR:s3:#f:f:dÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑÑ1ÑÑÃ/..'ÑÑ240,%1' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQí" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: s3: ' :ó ‚‹@þ SSn:¢Qc?ohtphd&&ÙÙÙÙÙÙÙÙÙÙ:¢ÙÙÙ ' :‹@þ SSn:¢Qöc?oaaaaaaaaaaaaaa1,2 -.1,201,-.301,ÙÙ0&&&&Í-.1,2aaaaaaaaaaaahtÙÙ:¢ÙÙÙÙÙÙÙ0&&&ÙÙÙÙÙÙÙ-1&&&ÙÙÙÙÙÙÙÙ$0&&&&ÍÙÙ&ÙÙÙÙÙÙÙ162&'&ÙÙØÙÙÙÙÙÙÙÙÙÙ0&&&ÙÙÙÙÙÙÙÙÙÙÙÙÙ4294967295&&&ÙÙÙÙA0&&&ÙÙÙÙÙÙÙÙÙÙÙÙ'å&&Ú&&&&ÙÙÙÙÙ ÙÙÙÙÙ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: ' :ó ‚‹@þ SSn:¢Qc?ohtphd&&ÙÙÙÙÙÙÙÙÙÙ:¢ÙÙÙ ' :‹@þ SSn:¢Qöc?oaaaaaaaaaaaaaa1,2 -.1,201,-.301,ÙÙ0&&&&Í-.1,2aaaaaaaaaaaahtÙÙ:¢ÙÙÙÙÙÙÙ0&&&ÙÙÙÙÙÙÙ-1&&&ÙÙÙÙÙÙÙÙ$0&&&&ÍÙÙ&ÙÙÙÙÙÙÙ162&'&ÙÙØÙÙÙÙÙÙÙÙÙÙ0&&&ÙÙÙÙÙÙÙÙÙÙÙÙÙ4294967295&&&ÙÙÙÙA0&&&ÙÙÙÙÙÙÙÙÙÙÙÙ'å&&Ú&&&&ÙÙÙÙÙ ÙÙÙÙÙ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=ID=*g Step #5: ##contig=ID=*g Step #5: ##contig=K\xC8535\x1EK\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8535\x1EK\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '##contig,=<' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=R:UdatUR:data:a:,>R:UR:data:a,>R:O%0á%$O%0a%_O%0a>/%ó:,>R:O%0á%_O%0a%_O%0a>/%ó ?O%0á%_O%0a>/%ó:Ô>R:O%0á%_O%0a%_O%0a>/%ó ?O%0á%_O%0a%_O%0a>/0a%_O%0a>/%ó ?a:a,>R:O%0á%_O%0a%º_O%0a>/%ó:smt,>R:O%0á%_O%0a%_%Z00a>/%ó:,.R:O%0á%_O%0a%.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>R:UdatUR:data:a:,>R:UR:data:a,>R:O%0á%$O%0a%_O%0a>/%ó:,>R:O%0á%_O%0a%_O%0a>/%ó ?O%0á%_O%0a>/%ó:Ô>R:O%0á%_O%0a%_O%0a>/%ó ?O%0á%_O%0a%_O%0a>/0a%_O%0a>/%ó ?a:a,>R:O%0á%_O%0a%º_O%0a>/%ó:smt,>R:O%0á%_O%0a%_%Z00a>/%ó:,.R:O%0á%_O%0a%' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ì' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ì" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ì' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ì" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '36u1,7,,,,,,,,,,,,,937-,,1100003,VC547758p,,,,,+922337287587592168' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=a:R' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>Oa%a:5a,>a:R' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to load reference #0 Step #5: [W::cram_encode_container] Enabling embed_ref=2 mode to auto-generate reference Step #5: [W::cram_encode_container] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "Ïÿ¹ÿÿÿS,ÏÏ://ÏÏÏ.ÏÏÏÏ.ÏÏÏÏÏÏÏÏÏÏÏHD" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "S[\x1FS"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "S[\x1FS"; treated as unmapped Step #5: [E::fai_build3_core] Failed to open the file s3.n./@SQ : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 's3.n./@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "S[\x1FS"; treated as unmapped Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "ù" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "8"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "8"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "8"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build3_core] Failed to open the file data:Sp:¤¨ : Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'data:Sp:¤¨' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 26 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 26 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 26 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:s%%: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:s%%' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:I array Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:I array Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: s3:f:data:6666666666666666contig666666666666666666666666666666666666666666666ÿ@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:data:6666666666666666contig666666666666666666666666666666666666666666666ÿ@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed data in B:I array Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [E::fai_build_core] File truncated at line 26 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔÖ ,@t %0ae%ОÔ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x19"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x19"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 14 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x19"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x19"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 14 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x19"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ\x19"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "daiai"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 14 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:S Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:S Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:S Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [E::cram_populate_ref] UR tags pointing to remote files are not supported Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [E::cram_populate_ref] UR tags pointing to remote files are not supported Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 3 Step #5: [E::fai_build_core] The last entry 'Oa%a:5a,>a:R' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>Oa%a:5a,>a:R' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to load reference #0 Step #5: [W::cram_encode_container] Enabling embed_ref=2 mode to auto-generate reference Step #5: [W::cram_encode_container] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [E::hts_hopen] Failed to open file data Step #5: s3:%%: ,@,#,ÿ70141. ,@,1?0#,ÿ4:: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:%%: ,@,#,ÿ70141. ,@,1?0#,ÿ4:' Step #5: [W::cram_get_ref] Failed to populate reference "Š:ÿÿÍ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 15 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 15 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "$"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 15 Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read SQ flag 1808 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " é" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 2441797773 for read "SQ " is too long Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ¶¶¶¶¶¶¶¶ flag 1808 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " é" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 1437031036 for read "¶¶¶¶¶¶¶¶" is too long Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read ¶¶¶¶¶¶¶¶ flag 1808 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " é" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 1437031036 for read "¶¶¶¶¶¶¶¶" is too long Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read SQ flag 1808 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " é" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 2441797773 for read "SQ " is too long Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'h(' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "h(" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '*' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "*" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at *:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '2' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "2" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'hZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'TZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'hRMAT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_filter] FILTER 'è' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ì' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ì" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTL' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '##filef' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "##filef" Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ì' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ì" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GTL' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'h(' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "h(" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig '*' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "*" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at *:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '2' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "2" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'hZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'TZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig 'I' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::vcf_parse_format_dict2] FORMAT 'hRMAT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO 'è' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "è" Step #5: [E::bcf_write] Broken VCF record, the number of columns at :0 does not match the number of samples (0 vs 1) Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::vcf_parse_filter] FILTER 'È€INFO' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FORMAT' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig ']' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "]" Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO 'L' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read #id flag 1808 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference " é" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 1787451130 for read "#id" is too long Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=ongi,I=ongi,I=ongi,I=ongi,I= %Ïa\%\\:Q : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file ':::%5ahttp0 %0iøÿþ::aþ@0QaiO%0aŸ > %Ïa\%\\:Q' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [E::parse_cigar] CIGAR length invalid at position 9 ( * ) Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xDB"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xDB"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xDB"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'P©ÿÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ZÿÿÿÿÿÿÔ^' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ZÿÿÿÿÿÿÔ^" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Gä?' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Gä?" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig 'z' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "z" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'P©ÿ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'P©ÿÿzZ' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "P©ÿÿzZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at z:0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'ZÿÿÿÿÿÿÔ^' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ZÿÿÿÿÿÿÔ^" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Gä?' at z:0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Gä?" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at z:0 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "ðUR:s3:s%%" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '　FIÿÿó „ÿÿ' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'INFO' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_filter] FILTER '　' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '　FIÿÿó „ÿÿ' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'INFO' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '　FIÿÿó „ÿÿ' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'INFO' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_filter] FILTER '　' is not defined in the header Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '　FIÿÿó „ÿÿ' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'INFO' is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%02ah)0:aO%1_______FFFFFFFFFF____________________________________________Ïÿ¹ÿÿ&>%02ah)0:aO%1__________________________________________Ïÿ¹ÿÿ&>%02ah)0:%aO%1a´Û¬¬¬¬¬°_____________:::ÿÿSSSSSSSS::callback&&$&665:;;x3a40,%1è: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:#f:f:dÑÑÑÑÑÑÑÑÑSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSShttphdr_cSSSdÑSSSSSSSSSSSSS__________________________________________Ïÿ¹ÿÿ&>%02ah)0:aO%1_______FFFFFFFFFF____________________________________________Ïÿ¹ÿÿ&>%02ah)0:aO%1__________________________________________Ïÿ¹ÿÿ&>%02ah)0:%aO%1a´Û¬¬¬¬¬°_____________:::ÿÿSSSSSSSS::callback&&$&665:;;x3a40,%1è' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQí" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10#i"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\xB3VCFv\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\x18\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 19 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10#i"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\xB3VCFv\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\x18\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 19 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10#i"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\xB3VCFv\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\x18\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 19 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "MC" Step #5: [W::bcf_hdr_parse] Could not parse header line: "n%YtC- " Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "MC" Step #5: [W::bcf_hdr_parse] Could not parse header line: "n%YtC- " Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=\xF3\xA0\x80\xA6\xA0=1,ID=00##fileformat=VCF,Z@=100\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hrec_check] Invalid tag name: "1000C" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##1000G>\xF3\xA0\x80\xA6" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=\xB6\xBB\xC2\xCF\xCF\xDC#filef/rmat=V\xB3\xB9\xD3\xA5\xBF\xC2\xCE\xCF0\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hrec_check] Invalid tag name: "11000G" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##1000100\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##201\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=\xF3\xA0\x80\xA6\xA0=1,ID=00##fileformat=VCF,Z@=100\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hrec_check] Invalid tag name: "1000C" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##1000G>\xF3\xA0\x80\xA6" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=\xB6\xBB\xC2\xCF\xCF\xDC#filef/rmat=V\xB3\xB9\xD3\xA5\xBF\xC2\xCE\xCF0\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hrec_check] Invalid tag name: "11000G" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##1000100\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##INFO=\xF3\xA0\x80\xA6"' Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##201\xD0\xB8\xC1\x07\xA0\x80\xA6" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_filter] FILTER 'FIL[ER' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'H' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '6<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "6<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::vcf_parse_info] Could not add dummy header for INFO '6<' at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=z--36-€ÿÿÿÿÿÿÿÿÿÿÿ5colt-46i&&>INFO=z655385,66fai8,,65531S,6pe=Flag,Typd=F,ag$###CO" Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3::::@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3::::@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3::::@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3::::@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "" with multiple LN: tag with different values. Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key DD Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿS Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿR Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key R= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Ø$ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Dþ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key #» Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key » Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key »c Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key D¢ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 09 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 71 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key v Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Ø Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÷D Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key [# Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key » Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key »» Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ry Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key t4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key h= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_TD] More than one TD block found in compression header Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: # Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key I# Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key fi Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ef Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ri Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key tÊ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key =V Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key FN Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key O= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key DD Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿS Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿR Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key R= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Ø$ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Dþ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key #» Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key » Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key »c Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key D¢ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 09 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 71 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key v Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Ø Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÷D Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key [# Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key » Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key »» Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ry Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key t4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key h= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_TD] More than one TD block found in compression header Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: # Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key I# Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key fi Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ef Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ri Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key tÊ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key =V Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key FN Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key O= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key DD Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿS Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿR Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key R= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Ø$ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Dþ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key #» Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key » Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key »c Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key D¢ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key  Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÿÿ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 09 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key 71 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key v Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Ø Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key @S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ÷D Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key [# Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key » Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key S Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key »» Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ry Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key t4 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key h= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key SQ Step #5: [W::cram_decode_TD] More than one TD block found in compression header Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: # Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key I# Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key fi Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ef Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ri Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key tÊ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key =V Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key FN Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key O= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%0ah)0:aO%1_______FFFFFFFFFF____________________________________________Ïÿ¹ÿÿ&>%02ah)170141183460469231731687303715884105728:aO%1_____________________________________ÿ_¹___Ïÿ_ÿ&>%02ah)0:%aO%1a´Û¬¬¬¬¬°_____________:::ÿÿSSSSSSSS::callback&&$&665:;;x6a1844073709551616,%1è: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:#f:f:dÑÑÑÑÑÑÑÑÑSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSShttphdr_cSSSdÑSSSSSSSSSSSSS__________________________________________Ïÿ¹ÿÿ&>%0ah)0:aO%1_______FFFFFFFFFF____________________________________________Ïÿ¹ÿÿ&>%02ah)170141183460469231731687303715884105728:aO%1_____________________________________ÿ_¹___Ïÿ_ÿ&>%02ah)0:%aO%1a´Û¬¬¬¬¬°_____________:::ÿÿSSSSSSSS::callback&&$&665:;;x6a1844073709551616,%1è' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQí" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "%\xDDYfJ#####" Step #5: [W::bcf_hdr_parse] Could not parse header line: "i|eformat=VCFW\xFC" Step #5: [W::bcf_hdr_parse] Could not parse header line: "" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contig=$dÛÆa" at byte offset 181 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "$dÛÆa" at byte offset 192 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 198 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 208 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 232 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 242 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 259 Step #5: [E::fai_build3_core] Failed to open FASTA index data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0,>za%1a%0%0d0a%0,,>z_:O%0a%_O.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0,>za%1a%0%0d0a%0,,>z_:O%0a%_O' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: gs:fŽÿÿÿÿmm–N:0:a%0ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿOO%>%1r@SO%1%|~-0aÛÏžÁ Ù°à0a>mÿÿÿÿÿÿÿÿÿAÿ,ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿBAM%ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmfaimmmmmmm-mmmmmmmmmmmmmmmmmmmmmmmmmTTTTTTTTTTTTTTTTmÿÿÿÿÿÿÿÿÿAÿ,ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿBAM%ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmfaimmmmmmm-mmmmmmmmmmmmmmmmmmmmmmm9>_: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'gs:fŽÿÿÿÿmm–N:0:a%0ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿOO%>%1r@SO%1%|~-0aÛÏžÁ Ù°à0a>mÿÿÿÿÿÿÿÿÿAÿ,ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿBAM%ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmfaimmmmmmm-mmmmmmmmmmmmmmmmmmmmmmmmmTTTTTTTTTTTTTTTTmÿÿÿÿÿÿÿÿÿAÿ,ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿBAM%ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿmmfaimmmmmmm-mmmmmmmmmmmmmmmmmmmmmmm9>_' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] CIGAR and query sequence are of different length Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:///­//////?%0a%0a%0d%0a%0@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:///­//////?%0a%0a%0d%0a%0@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [E::process_one_read] Unknown CIGAR op code 9 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 48 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 48 operators at the CG tag Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 48 operators at the CG tag Step #5: [E::process_one_read] Unknown CIGAR op code 12 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] SEQ and QUAL are of different length Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::cram_populate_ref] UR tags pointing to remote files are not supported Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::process_one_read] Unknown CIGAR op code 9 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=ÿÿÿÿÿÿÿ#idx##701418?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ Y: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:%%: ,fail_on_errorr@,#,#,ÿ550608?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ,#,ÿ701418?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ------------------------------------------------------------ÿ550608?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ,#,ÿ701418?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ----------------------------------------------------------------------------ÿÿÿÿÿÿ ø----------ÿ0------þ@,#,ÿ550608?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ>ÿÿÿÿÿÿÿ#idx##701418?ÿ¿ÿ&ÿÿÿÿÿÿÿÿÿÿÿÿÿÿ Y' Step #5: [W::cram_get_ref] Failed to populate reference "ŠQí" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 20 Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_parse1] unrecognized reference name "dai"; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "SQ"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 20 Step #5: [W::cram_get_ref] Failed to populate reference "JÿòÿÿÿÿÿÿÿÿÿÿÿÿÿÿxéóVCFvWÿ,ÛÿQ£ªªªLêxÿÉþ%R" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3: -' :‹@þ SSn:¢Qc?fqiphfaÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ======================================================================================================ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ===========================================================================================ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ™™™™™¹™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: -' :‹@þ SSn:¢Qc?fqiphfaÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ======================================================================================================ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ===========================================================================================ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ™™™™™¹™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™™' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_decode_compression_header] Unrecognised key: i Step #5: [W::cram_decode_compression_header] Unrecognised key: ?& Step #5: [W::cram_decode_compression_header] Unrecognised key: ¾À Step #5: [W::cram_decode_compression_header] Unrecognised key: ù4 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: FA Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: -- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [E::cram_beta_decode_init] Malformed beta header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: i Step #5: [W::cram_decode_compression_header] Unrecognised key: ?& Step #5: [W::cram_decode_compression_header] Unrecognised key: ¾À Step #5: [W::cram_decode_compression_header] Unrecognised key: ù4 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: FA Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: -- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [E::cram_beta_decode_init] Malformed beta header stream Step #5: [W::cram_decode_compression_header] Unrecognised key: i Step #5: [W::cram_decode_compression_header] Unrecognised key: ?& Step #5: [W::cram_decode_compression_header] Unrecognised key: ¾À Step #5: [W::cram_decode_compression_header] Unrecognised key: ù4 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: FA Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: -- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [E::cram_beta_decode_init] Malformed beta header stream Step #5: [W::cram_get_ref] Failed to populate reference "Ïÿ¹ÿÿ&&&/›//,,,,,,,,’’’’’;;;;;_:ÿÿÿÿaO%_O%0&a>%5B¸ýþaO@9a¡R³:0ŸO%;1920VCFv«««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««««ÿÿÿBAM0B¸ýþaO@1ai41-,-&$&&,ü2<:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_decode_compression_header] Unrecognised key: i Step #5: [W::cram_decode_compression_header] Unrecognised key: ?& Step #5: [W::cram_decode_compression_header] Unrecognised key: ¾À Step #5: [W::cram_decode_compression_header] Unrecognised key: ù4 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: FA Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: -- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: i Step #5: [W::cram_decode_compression_header] Unrecognised key: ?& Step #5: [W::cram_decode_compression_header] Unrecognised key: ¾À Step #5: [W::cram_decode_compression_header] Unrecognised key: ù4 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: FA Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: -- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: i Step #5: [W::cram_decode_compression_header] Unrecognised key: ?& Step #5: [W::cram_decode_compression_header] Unrecognised key: ¾À Step #5: [W::cram_decode_compression_header] Unrecognised key: ù4 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: FA Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: -- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::cram_decode_compression_header] Codec for key BA defined more than once Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] CIGAR and query sequence are of different length Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:///­//////?/%0a%0a%0d%0a%0@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:///­//////?/%0a%0a%0d%0a%0@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:aA_0ad%O>:ataARf_OO%0a%0a>_&O%0a>%N:0a%0a>%ÿÿ %0a%0a> %0O%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a+%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:aA_0ad%O>:ataARf_OO%0a%0a>_&O%0a>%N:0a%0a>%ÿÿ %0a%0a> %0O%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a+%1r@SO%1%~-t0a%0a> %0aiR:sa%0a#%0a>_O%0a>%1r@SO%1%~-t0a%0a> %0aiR:' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig '#CHRO7ó2ó6 ó ,=,,,,,,,,,,,®,,' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO= file.sam` Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::cram_get_ref] Failed to populate reference "Ïÿ¹ÿÿÿS.9+23371203967972ø€ÿ2@SQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##IN*O= Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key e Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key რStep #5: [W::cram_decode_compression_header] Unrecognised preservation map key 3 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key / Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key š Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ~ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key :> Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key e Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key რStep #5: [W::cram_decode_compression_header] Unrecognised preservation map key 3 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key / Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key š Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ~ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key :> Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key Step #5: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key e Step #5: Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:i Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:i Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Malformed B:i Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: s3:f:data:6666666666666666666666666666666666666666666666666666666666666666666ÿ@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:data:6666666666666666666666666666666666666666666666666666666666666666666ÿ@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [E::cram_generate_reference] Cannot build reference with unsorted data Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "S[\x1FS"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "S[\x1FS"; treated as unmapped Step #5: [E::fai_build3_core] Failed to open the file s3.n./@SQ%SN:TyN: ÿA]# : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 's3.n./@SQ%SN:TyN: ÿA]#' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "S[\x1FS"; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [E::cram_generate_reference] Cannot build reference with unsorted data Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [E::sam_hrecs_error] Header line does not have a two character key at line 3: "@S 2¢ÿÿrrrrrrrrrrrrrr" Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "WN:@SQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ""; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "["; treated as unmapped Step #5: #2048 pulse exec/s: 128 rss: 1327Mb Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::aux_parse] invalid aux tag id Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_generate_reference] Cannot build reference with unsorted data Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\x05\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\x05\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\x05\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_put_bam_seq] Changing from embed_ref to no_ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 5 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #4/5 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::cram_encode_container] Keeping non-ref mode from now on Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.1\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "\xFF\x7F"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.1\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "\xFF\x7F"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.1\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\x10\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "\xFF\x7F"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO= file.sam` Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=" Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=<=" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=<=" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##IN>&-&&>&mdR\xCA\xCA\xCA\xCAz\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xFFi,-\tA:TI,-1\t\t216\t\t0S\t[\t\t\t\t\xFF\xFF\xFF,--\tTA:I,-\tTA:i,-\t:TAI,-42#C" Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=<=" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=" Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=<=" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##IN>&-&&>&mdR\xCA\xCA\xCA\xCAz\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xCA\xFFi,-\tA:TI,-1\t\t216\t\t0S\t[\t\t\t\t\xFF\xFF\xFF,--\tTA:I,-\tTA:i,-\t:TAI,-42#C" Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 10 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 10 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "2ü¬Ä;;h}SÄ0;m;@ÍFFß;=ß;HF=;@+;FFÿÿÿcu;oºmte;PA;Ô;ûubm-‰@;âr;ÿÿ{2;ÿÿÅ;ĽH;@¶;ßÊ;FF@;@ÝÄä;Ã1;EÄÄÄÄÀ;ŠI;ÿÿÿÄ;Ä@¶" with multiple LN: tag with different values. Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [W::vcf_parse_filter] FILTER 'È€INFO' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'FORMAT' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse] Contig ']' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "]" Step #5: [W::vcf_parse_filter] FILTER 'È€' is not defined in the header Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '##idx##' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "##idx##" Step #5: [W::vcf_parse_info] INFO 'L' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_filter] FILTER ':' is not defined in the header Step #5: [W::vcf_parse_info] INFO '+' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "+" Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '8<' is not defined in the header, assuming Type=String Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L/FIL' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L/FIL" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##FORMAT=] Step #5: [0] Step #5: [W::bcf_hrec_check] Invalid tag name: "8<,Number=1,Type=String,Description="Dummy">" Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Type defined. Assuming String Step #5: [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' Step #5: [W::vcf_parse_info] INFO '0L' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "0L" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [E::hts_hopen] Failed to open file data Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##IN*O=:À`:AÒ>&-),,,0000forÐat=V_C,-000fqi flag 0 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "ù" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::cram_put_bam_seq] CIGAR query length 2324376641 for read "&]&&15i&&>:À`:AÒ>&-),,,0000forÐat=V_C,-000fqi" is too long Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:a<_1ÿÿÿÿÿÿäO%Ш%RR>_&O_%0a>%%a#%0a>_O%0>a ZZZ¦¥¥¡@' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 4 Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "2ü¬Ä;;h}SÄ0;" with multiple LN: tag with different values. Step #5: [E::hts_hopen] Failed to open file data Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "••,,$ÿÿÿÿSQ" with multiple LN: tag with different values. Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##conmemtig=' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##contig=>"' Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not add dummy header for contig '>' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:a<_1ÿÿÿÿÿÿäO%Ш%RR>_&O_%0a>%%a#%0a>_O%0>a ZZZ¦¥¥¡@' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:a<_1ÿÿÿÿÿÿäO%Ш%RR>_&O_%0a>%%a#%0a>_O%0>a ZZZ¦¥¥¡@' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xAC\xAC\xAC\xAC\xAC\xAC\xAC\xAC\x"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "••,,,ÿÿÿÿoQ" with multiple LN: tag with different values. Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz?1."; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz?1."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz?1."; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz?1."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz?1."; treated as unmapped Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz?1."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 7 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:///////phd6&ÙÙÿ7##f: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:///////phd6&ÙÙÿ7##f' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3:///////phd6&ÙÙÿ7##f: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:///////phd6&ÙÙÿ7##f' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] CIGAR and query sequence are of different length Step #5: [W::sam_read1_sam] Parse error at line 10 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse1] CIGAR and query sequence are of different length Step #5: [W::sam_read1_sam] Parse error at line 10 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: ==50== ERROR: libFuzzer: out-of-memory (used: 2185Mb; limit: 2048Mb) Step #5: To change the out-of-memory limit use -rss_limit_mb= Step #5: Step #5: MS: 0 ; base unit: 0000000000000000000000000000000000000000 Step #5: artifact_prefix='./'; Test unit written to ./oom-d65d2b4d245a732a7026ef7aa6d117049623766b Step #5: SUMMARY: libFuzzer: out-of-memory Step #5: MERGE-OUTER: attempt 3 Step #5: INFO: Running with entropic power schedule (0xFF, 100). Step #5: INFO: Seed: 1089462899 Step #5: INFO: -max_len is not provided; libFuzzer will not generate inputs larger than 1048576 bytes Step #5: MERGE-INNER: using the control file '/tmp/libFuzzerTemp.Merge39.txt' Step #5: MERGE-INNER: '/corpus/hts_open_fuzzer/d65d2b4d245a732a7026ef7aa6d117049623766b' caused a failure at the previous merge step Step #5: MERGE-INNER: 7595 total files; 6215 processed earlier; will process 1380 files now Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2\x10\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",.02f\xFF\x10\x10\x10\x10\x10\x10\"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\x18\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 27 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2\x10\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",.02f\xFF\x10\x10\x10\x10\x10\x10\"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\x18\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 27 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFF\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [E::cram_generate_reference] Cannot build reference with unsorted data Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_put_bam_seq] Changing from embed_ref to no_ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2\x10\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",TD2,.01\xFF\x10\x10\x10\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx##\x12\x10\x10\x10\xFF\xFF\xF"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",.02f\xFF\x10\x10\x10\x10\x10\x10\"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\xFFP\x18\x10\x10\xFF\xFF\xFF\xF9"; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF01,-\xFF\xFF\x10\x18\x10\x10\x"...; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query must have a CIGAR; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "##idx"; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 27 Step #5: #1 pulse exec/s: 0 rss: 38Mb Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "M\x01)" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x99ntC-!" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4283825976: Invalid CONTIG id 1054976 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4283825976: Invalid ID type 9 (unknown) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4283825976: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4283825976: Invalid INFO id 52232960 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4283825976 - shared section malformed or too short Step #5: [W::bcf_hdr_parse] The first line should be ##fileformat; is the VCF/BCF header broken? Step #5: [W::bcf_hdr_parse] Could not parse header line: "M\x01)" Step #5: [W::bcf_hdr_parse] Could not parse header line: "\x99ntC-!" Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_hdr_get_version] No version string found, assuming VCFv4.2 Step #5: [W::bcf_record_check] Bad BCF record at 4283825976: Invalid CONTIG id 1054976 Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4283825976: Invalid ID type 9 (unknown) Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4283825976: No REF allele Step #5: [W::bcf_record_check] Bad BCF record at (unknown):4283825976: Invalid INFO id 52232960 Step #5: [E::bcf_record_check] Bad BCF record at (unknown):4283825976 - shared section malformed or too short Step #5: #2 pulse exec/s: 0 rss: 38Mb Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##INFO=z_:O%0aO %0A>1##›#˜#x%d%0a%%_O%0A>%d%0[a%ÿ˜›x##%d%0a%%_O%0A>%d%0##%d%0a%%_O%0A>%d%0a%ÿÿÿÿCRAMÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿa:a®a:aÚ:,>ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ"z_:O%5aO%0A0A>##%d%0a%%_O%0A>%d%×ääääääähttp_response[í%ÿ˜›x##%d%0a%%_O%0A>%d%0#"˜›x##a%ÿÿýÿCRAMÿÿÿa:aÚ:,>ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ"z_:O%0aO%0A>##˜›x##%d##›#˜#x%d%0a%%_O%0A>%d%0a%ÿ˜›x##%d%0a%%_O%0A>%d%0##˜›x##%d%0a%%_% O: %5aO%0A>##˜›x##%d%0a% N:*LN:;ÿÿN:' Step #5: [W::cram_get_ref] Failed to populate reference "*LN:;ÿÿN:" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:" " in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"@" in sam header Step #5: [W::sam_hrecs_add_ref_altnames] Duplicate entry AN:"#" in sam header Step #5: [W::cram_get_ref] Failed to populate reference "Ïÿ¹ÿÿÿS,ÏÏÏÏÏÏÏÏ.ÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏŽÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏÏ9+233712039679" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_get_ref] Failed to populate reference "-43423ö8 12SQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'AN2:D:id' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '1E' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '$' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'INFO' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ÕÕÕ@SQ' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ÕÕÕ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÕÕÕ" Step #5: [W::vcf_parse_info] INFO '&' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "&" Step #5: [W::vcf_parse_info] INFO '?' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "?" Step #5: [W::vcf_parse_info] INFO '#' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "#" Step #5: [W::vcf_parse_info] INFO 'CRAM¼ÿòÿ€ÿB¾AIilc' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "CRAM¼ÿòÿ€ÿB¾AIilc" Step #5: [W::vcf_parse_info] INFO 'trDcÄÄÄÄ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "trDcÄÄÄÄ" Step #5: [W::vcf_parse_info] INFO 'ÄÄ`ŠI½½½' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÄÄ`ŠI½½½" Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::vcf_parse_info] INFO 'tß' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "tß" Step #5: [W::vcf_parse_info] INFO 'F' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO 'F@F©7' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "F@F©7" Step #5: [W::vcf_parse_info] INFO 'M:m:emr-ODeS2:1-3¤¤¤mü' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "M:m:emr-ODeS2:1-3¤¤¤mü" Step #5: [W::vcf_parse_info] INFO '1' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "1" Step #5: [W::vcf_parse_info] INFO 'ü¬Ä' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ü¬Ä" Step #5: [W::vcf_parse_info] INFO '!`--S]ÐÐÐÐÐÐÐÐ-' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "!`--S]ÐÐÐÐÐÐÐÐ-" Step #5: [W::vcf_parse_info] INFO '*--h}SÄ0' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "*--h}SÄ0" Step #5: [W::vcf_parse_info] INFO 'krO3•fai' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "krO3•fai" Step #5: [W::vcf_parse_info] INFO '@F+' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@F+" Step #5: [W::vcf_parse_info] INFO 'FF' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '@###INFO' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@###INFO" Step #5: [W::vcf_parse_info] INFO '.F..' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ".F.." Step #5: [W::vcf_parse_info] INFO '•' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "•" Step #5: [W::vcf_parse_info] INFO '@CRAM' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@CRAM" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER 'AN2:D:id' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '1E' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER '$' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'INFO' is not defined in the header Step #5: [W::vcf_parse_filter] FILTER 'ÕÕÕ@SQ' is not defined in the header Step #5: [W::vcf_parse_info] INFO 'ÕÕÕ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÕÕÕ" Step #5: [W::vcf_parse_info] INFO '&' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "&" Step #5: [W::vcf_parse_info] INFO '?' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "?" Step #5: [W::vcf_parse_info] INFO '#' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "#" Step #5: [W::vcf_parse_info] INFO 'CRAM¼ÿòÿ€ÿB¾AIilc' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "CRAM¼ÿòÿ€ÿB¾AIilc" Step #5: [W::vcf_parse_info] INFO 'trDcÄÄÄÄ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "trDcÄÄÄÄ" Step #5: [W::vcf_parse_info] INFO 'ÄÄ`ŠI½½½' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ÄÄ`ŠI½½½" Step #5: [W::vcf_parse_info] INFO '@' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@" Step #5: [W::vcf_parse_info] INFO 'tß' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "tß" Step #5: [W::vcf_parse_info] INFO 'F' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO 'F@F©7' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "F@F©7" Step #5: [W::vcf_parse_info] INFO 'M:m:emr-ODeS2:1-3¤¤¤mü' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "M:m:emr-ODeS2:1-3¤¤¤mü" Step #5: [W::vcf_parse_info] INFO '1' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "1" Step #5: [W::vcf_parse_info] INFO 'ü¬Ä' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ü¬Ä" Step #5: [W::vcf_parse_info] INFO '!`--S]ÐÐÐÐÐÐÐÐ-' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "!`--S]ÐÐÐÐÐÐÐÐ-" Step #5: [W::vcf_parse_info] INFO '*--h}SÄ0' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "*--h}SÄ0" Step #5: [W::vcf_parse_info] INFO 'krO3•fai' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "krO3•fai" Step #5: [W::vcf_parse_info] INFO '@F#' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@F#" Step #5: [W::vcf_parse_info] INFO 'FF' is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_info] INFO '@###INFO' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@###INFO" Step #5: [W::vcf_parse_info] INFO '.F..' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ".F.." Step #5: [W::vcf_parse_info] INFO '•' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "•" Step #5: [W::vcf_parse_info] INFO '@CRAM' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "@CRAM" Step #5: [W::vcf_parse_info] INFO '!`--S]ÐÐÐ' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "!`--S]ÐÐÐ" Step #5: [E::vcf_parse] Could not parse the position ',,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::bcf_write] Unchecked error (1 Contig not defined in header) at :0 Step #5: [W::cram_get_ref] Failed to populate reference ":::;@SQ" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '*' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [E::vcf_parse] Could not parse the position 'C@' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '*' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=z_:a<_1ÿÿÿÿÿÿäO%Ш%RR>_&O_%0a>%%a#%0a>_O%0>a ZZZ¦¥¥¡@' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=" Step #5: [E::vcf_parse] Could not add dummy header for contig 'n%Y,-tC2-!' Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=a:R' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:,>Oa%a:5a,>a:R' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to load reference #0 Step #5: [W::cram_encode_container] Enabling embed_ref=2 mode to auto-generate reference Step #5: [W::cram_encode_container] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: s3:f:data:6666666666666666666666666666666666666666666666666666666666666666666ÿ@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:f:data:6666666666666666666666666666666666666666666666666666666666666666666ÿ@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "••,,,ÿÿÿÿoQ" with multiple LN: tag with different values. Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:;;;;;;&&&0Ÿ&&³±ÌO%0a_:ÿÿÿO%_aÿO%0&a>fai%_aÿ(%0&a>fai¸ýþaÏ@0a¡R³:00&a>%0B?þaO@?;;’’’’’’’’’?1’;;;;;;;;;;;;& &0’’’’’’’’’&1’;;;;;;;;;ÿÿÌÌÌÌÌÌÌÌÌÌÌÌþÿ&fai%0&a>%65536B?AþaO@;;;’ó ’’€;&& &0’’’’È’’’’’&1’;;;;;;;;;ÿÿÿÿÿÿ¡R³:00&a>%0B?þaO@;;;’’’’’’’’’&1’;;;;;;;;;;;;;;;&&$&&&&þÿ&fai%0&a>%65536B?Aþš°¿Ä;;’ó ’’€;&& &0’’’’’’’’’&1’;;;;;;;;;ÿÿÿÿÿÿÿ;x-amz-content-;;;;;&&$&Ÿ&&³±ÌO%0$&&&&&//;&&$Ì1_:ÿÿÿž°Ú O%0$&&;&&&//&&$&&&&&/&&$&Ÿ&&³±ÌO%0$&&&?AþaO@;;;’ó ’’€;&& &0’’’’È’’’’’&1’;;;;;;;;’’’’’’’’’&1’;;;;;;;;;ÿÿÿÿÿÿÿ;x-amz-content-;;;;;&&$&Ÿ&&³±ÌO%0$&&&&&//;&&$&&&&&///&&&&////,,,,,,,â€É’ÿÿÿÿÿÿÿÿÿÿÿÿÿÿOÿa%Ì1_:ÿÿÿž°Ú O%0$&&&&&//;&&$&&&&&/&&$&Ÿ&&³±ÌO%0$&&&&&//;&&$&&&&&/1//&&&&////,,,,,,,â€É’ÿÿÿÿÿÿÿÿÿÿÿÿÿÿOÿa%Ì1_:ÿ;;;;;;;;;&&///&&&&////,: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:;;;;;;&&&0Ÿ&&³±ÌO%0a_:ÿÿÿO%_aÿO%0&a>fai%_aÿ(%0&a>fai¸ýþaÏ@0a¡R³:00&a>%0B?þaO@?;;’’’’’’’’’?1’;;;;;;;;;;;;& &0’’’’’’’’’&1’;;;;;;;;;ÿÿÌÌÌÌÌÌÌÌÌÌÌÌþÿ&fai%0&a>%65536B?AþaO@;;;’ó ’’€;&& &0’’’’È’’’’’&1’;;;;;;;;;ÿÿÿÿÿÿ¡R³:00&a>%0B?þaO@;;;’’’’’’’’’&1’;;;;;;;;;;;;;;;&&$&&&&þÿ&fai%0&a>%65536B?Aþš°¿Ä;;’ó ’’€;&& &0’’’’’’’’’&1’;;;;;;;;;ÿÿÿÿÿÿÿ;x-amz-content-;;;;;&&$&Ÿ&&³±ÌO%0$&&&&&//;&&$Ì1_:ÿÿÿž°Ú O%0$&&;&&&//&&$&&&&&/&&$&Ÿ&&³±ÌO%0$&&&?AþaO@;;;’ó ’’€;&& &0’’’’È’’’’’&1’;;;;;;;;’’’’’’’’’&1’;;;;;;;;;ÿÿÿÿÿÿÿ;x-amz-content-;;;;;&&$&Ÿ&&³±ÌO%0$&&&&&//;&&$&&&&&///&&&&////,,,,,,,â€É’ÿÿÿÿÿÿÿÿÿÿÿÿÿÿOÿa%Ì1_:ÿÿÿž°Ú O%0$&&&&&//;&&$&&&&&/&&$&Ÿ&&³±ÌO%0$&&&&&//;&&$&&&&&/1//&&&&////,,,,,,,â€É’ÿÿÿÿÿÿÿÿÿÿÿÿÿÿOÿa%Ì1_:ÿ;;;;;;;;;&&///&&&&////,' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hrec_check] Missing ID attribute in one or more header lines Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##contpg=z_:O%0a%_OO%0A>%d%0a%0,>z_:O%0a%_O%0A>%d%0a%%_O%0A>%d%0a%0a%0A>%d%0a%0ÿa>ÿ:ÿO%1701411834604692,>z@SQ.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aa:aÚ:,>z_:O%0a%_OO%0A>%d%0a%0,>z_:O%0a%_O%0A>%d%0a%%_O%0A>%d%0a%0a%0A>%d%0a%0ÿa>ÿ:ÿO%1701411834604692,>z@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=$dÛÆa" at byte offset 162 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 181 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 211 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "$dÛÆa" at byte offset 256 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 262 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 272 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 294 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 300 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 355 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 361 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%ÿÿÿÿO%0}A>$dÛÆa" at byte offset 392 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "0a" at byte offset 402 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 406 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "$dÛÆa" at byte offset 434 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 440 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 450 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 487 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 504 Step #5: [E::fai_build3_core] Failed to open FASTA index data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$daÆ%0Ûa%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿ%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%O%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0´aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0,>za%1a%0%0d0a%0,,.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$daÆ%0Ûa%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿ%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%O%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0´aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0,>za%1a%0%0d0a%0,,' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: /A Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: B" Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: ,L Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: A0 Step #5: [W::cram_decode_compression_header] Unrecognised key: A0 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: HQ Step #5: [W::cram_decode_compression_header] Unrecognised key: / Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: BL Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: LQ Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: H, Step #5: [W::cram_decode_compression_header] Unrecognised key: +* Step #5: [W::cram_decode_compression_header] Unrecognised key: $$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $* Step #5: [W::cram_decode_compression_header] Unrecognised key: L$ Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Unrecognised key: ! Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key: ,U Step #5: [W::cram_decode_compression_header] Unrecognised key: ,U Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: LP Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: L, Step #5: [W::cram_decode_compression_header] Unrecognised key: BL Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: * Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: $* Step #5: [W::cram_decode_compression_header] Unrecognised key: * Step #5: [W::cram_decode_compression_header] Unrecognised key: HQ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: : Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: \" Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: U Step #5: [W::cram_decode_compression_header] Unrecognised key: "P Step #5: [W::cram_decode_compression_header] Unrecognised key: UH Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: 1I Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: /\ Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: $, Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: $% Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: /A Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: B" Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: ,L Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: A0 Step #5: [W::cram_decode_compression_header] Unrecognised key: A0 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: HQ Step #5: [W::cram_decode_compression_header] Unrecognised key: / Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: BL Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: LQ Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: H, Step #5: [W::cram_decode_compression_header] Unrecognised key: +* Step #5: [W::cram_decode_compression_header] Unrecognised key: $$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $* Step #5: [W::cram_decode_compression_header] Unrecognised key: L$ Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Unrecognised key: ! Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key: ,U Step #5: [W::cram_decode_compression_header] Unrecognised key: ,U Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: LP Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: L, Step #5: [W::cram_decode_compression_header] Unrecognised key: BL Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: * Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: $* Step #5: [W::cram_decode_compression_header] Unrecognised key: * Step #5: [W::cram_decode_compression_header] Unrecognised key: HQ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: : Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: \" Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: U Step #5: [W::cram_decode_compression_header] Unrecognised key: "P Step #5: [W::cram_decode_compression_header] Unrecognised key: UH Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: 1I Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: /\ Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: $, Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: $% Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: /A Step #5: [W::cram_decode_compression_header] Unrecognised key: %7 Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: B" Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: ,L Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: A0 Step #5: [W::cram_decode_compression_header] Unrecognised key: A0 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: HQ Step #5: [W::cram_decode_compression_header] Unrecognised key: / Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: BL Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: LQ Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: H, Step #5: [W::cram_decode_compression_header] Unrecognised key: +* Step #5: [W::cram_decode_compression_header] Unrecognised key: $$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $* Step #5: [W::cram_decode_compression_header] Unrecognised key: L$ Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Unrecognised key: + Step #5: [W::cram_decode_compression_header] Unrecognised key: ! Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key: ,U Step #5: [W::cram_decode_compression_header] Unrecognised key: ,U Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: LP Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: L, Step #5: [W::cram_decode_compression_header] Unrecognised key: BL Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: * Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: $* Step #5: [W::cram_decode_compression_header] Unrecognised key: * Step #5: [W::cram_decode_compression_header] Unrecognised key: HQ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: : Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: \" Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: U Step #5: [W::cram_decode_compression_header] Unrecognised key: "P Step #5: [W::cram_decode_compression_header] Unrecognised key: UH Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: % Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: 1I Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: /\ Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: $, Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: $I Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: $% Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: s3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #4/5 Step #5: s3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:s %vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##IN*O= Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: >" Step #5: [W::cram_decode_compression_header] Unrecognised key: 'H Step #5: [W::cram_decode_compression_header] Unrecognised key: "$ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 9 Step #5: [W::cram_decode_compression_header] Unrecognised key: ]7 Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: AA Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: I7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: A Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: IL Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: U7 Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: @' Step #5: [W::cram_decode_compression_header] Unrecognised key: A\ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: LA Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: ]@ Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: ]- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: " Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: L" Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: B' Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: R Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: MH Step #5: [W::cram_decode_compression_header] Unrecognised key: ]\ Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: I Step #5: [W::cram_decode_compression_header] Unrecognised key: B' Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: A\ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: UB Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: "] Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: \] Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: >" Step #5: [W::cram_decode_compression_header] Unrecognised key: 'H Step #5: [W::cram_decode_compression_header] Unrecognised key: "$ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 9 Step #5: [W::cram_decode_compression_header] Unrecognised key: ]7 Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: AA Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: I7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: A Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: IL Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: U7 Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: @' Step #5: [W::cram_decode_compression_header] Unrecognised key: A\ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: LA Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: ]@ Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: B% Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: ]- Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: " Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: L" Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: B' Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: R Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: MH Step #5: [W::cram_decode_compression_header] Unrecognised key: ]\ Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: I Step #5: [W::cram_decode_compression_header] Unrecognised key: B' Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: A\ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: "U Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: UB Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: "] Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: \] Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: >" Step #5: [W::cram_decode_compression_header] Unrecognised key: 'H Step #5: [W::cram_decode_compression_header] Unrecognised key: "$ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 9 Step #5: [W::cram_decode_compression_header] Unrecognised key: ]7 Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: AA Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: I7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: H' Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: A Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: IL Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: U7 Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: @' Step #5: [W::cram_decode_compression_header] Unrecognised key: A\ Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##`=z_:a%_0ad%O>0_%0a0ahR:2O%1aL%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0N:O%0a%0a>%0N:O%0a%0a>_O%0a>%0rtma0aiR:2O%1ÿÿÿNat1aLN:O%0a%0a>%0N:O%0a%0O%0aÿ %0a%0a> %0R:2O%1aLN:O%0a%1a>_O%0a%0a>_O%0aiR:Oó —%¬a%aO>%0_%0a0ahR:2O%1aL%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0N:O%0a%0a>%0N:O%0a%0a>_O.%0a>%0rtma0aiR:2O%1ÿÿÿN:O%0aÞΞÁ_O%0a%0a>_O%0aÿ %0a%0a> %0aiR:saiR:O%0aa>_O%0a%0a>_O%0aÿ %0a%0a> %0aiR:saiR:O%0a%_O%0a>>_O%0a%0a>_O%0aÿ %0a%0a>data:aÚ:,>z_:a%_0ad%O>0_%0a0ahR:2O%1aL%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0N:O%0a%0a>%0N:O%0a%0a>_O%0a>%0rtma0aiR:2O%1ÿÿÿN:O%0a%1a>_O%0a%0a>_O%0aÿ %0a%0a> %0aiR:saiR:O%0aa>_O%0a%0a>_O%0aÿ %0a%0a> %0aiR:saiR:O:at1aLN:O%0a%0a>%0N:O%0a%0O%0aÿ %0a%0a> %0R:2O%1aLN:O%0a%1a>_O%0a%0a>_O%0aiR:Oó —%¬a%aO>%0_%0a0ahR:2O%1aL%0a>%0a0aiR:2O%1aLN:O%0a%0a>%0N:O%0a%0a>%0N:O%0a%0a>_O.%0a>%0r %0aiR:saiR:OO%0aÿ %0a%0a> %0aiR:saiR:O%0a%_O%0a>%0a' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3:;;;;;aiR³:0ŸO%941-,-&$&&,ü2<:: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:;;;;;aiR³:0ŸO%941-,-&$&&,ü2<:' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 18 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 18 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 24 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 24 Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 24 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 24 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 23 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 23 Step #5: [E::fai_build_core] The last entry 'zz_:a@SQ' has no sequence at line 7 Step #5: [E::refs_load_fai] Failed to open reference file 'data:a:a:ÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÌÿÿÿÿÌÌÌÌÌÌÌÌÌÌÌÌÌÌ,>z_:a%_]aARfa@Z%0a%_,>z_:a%_O%0Oúÿÿÿÿÿÿÿ%0a>:datfAa½ac@Z%0a._O%0a> *0aAR:daiRO%0a%_O%0a>zz_:a@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\r"; treated as unmapped Step #5: [E::read_ncigar] No CIGAR operations Step #5: [W::sam_read1_sam] Parse error at line 23 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: LA Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: ]@ Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: H> Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: '> Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: "J Step #5: [W::cram_decode_compression_header] Unrecognised key: UH Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: \" Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: ]B Step #5: [W::cram_decode_compression_header] Unrecognised key: IE Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: 'M Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: J' Step #5: [W::cram_decode_compression_header] Unrecognised key: 7L Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: @7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: 7H Step #5: [W::cram_decode_compression_header] Unrecognised key: U7 Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: E] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: V] Step #5: [W::cram_decode_compression_header] Unrecognised key: 7M Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: I\ Step #5: [W::cram_decode_compression_header] Unrecognised key: /I Step #5: [W::cram_decode_compression_header] Unrecognised key: /I Step #5: [W::cram_decode_compression_header] Unrecognised key: '! Step #5: [W::cram_decode_compression_header] Unrecognised key: !4 Step #5: [W::cram_decode_compression_header] Unrecognised key: B9 Step #5: [W::cram_decode_compression_header] Unrecognised key: 'U Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: ]- Step #5: [W::cram_decode_compression_header] Unrecognised key: LT Step #5: [W::cram_decode_compression_header] Unrecognised key: LB Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: L" Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: "M Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: I7 Step #5: [W::cram_decode_compression_header] Unrecognised key: JL Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: UB Step #5: [W::cram_decode_compression_header] Unrecognised key: 'I Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: LA Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: ]@ Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: H> Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: '> Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: "J Step #5: [W::cram_decode_compression_header] Unrecognised key: UH Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: \" Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: ]B Step #5: [W::cram_decode_compression_header] Unrecognised key: IE Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: 'M Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: J' Step #5: [W::cram_decode_compression_header] Unrecognised key: 7L Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: @7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: 7H Step #5: [W::cram_decode_compression_header] Unrecognised key: U7 Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: E] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: V] Step #5: [W::cram_decode_compression_header] Unrecognised key: 7M Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: I\ Step #5: [W::cram_decode_compression_header] Unrecognised key: /I Step #5: [W::cram_decode_compression_header] Unrecognised key: /I Step #5: [W::cram_decode_compression_header] Unrecognised key: '! Step #5: [W::cram_decode_compression_header] Unrecognised key: !4 Step #5: [W::cram_decode_compression_header] Unrecognised key: B9 Step #5: [W::cram_decode_compression_header] Unrecognised key: 'U Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: ]- Step #5: [W::cram_decode_compression_header] Unrecognised key: LT Step #5: [W::cram_decode_compression_header] Unrecognised key: LB Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: L" Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: "M Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: I7 Step #5: [W::cram_decode_compression_header] Unrecognised key: JL Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: UB Step #5: [W::cram_decode_compression_header] Unrecognised key: 'I Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: 'L Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: LA Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U@ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: ]@ Step #5: [W::cram_decode_compression_header] Unrecognised key: UT Step #5: [W::cram_decode_compression_header] Unrecognised key: H> Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: '> Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: "J Step #5: [W::cram_decode_compression_header] Unrecognised key: UH Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: \" Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: [W::cram_decode_compression_header] Unrecognised key: X Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: ]B Step #5: [W::cram_decode_compression_header] Unrecognised key: IE Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: 'M Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: J' Step #5: [W::cram_decode_compression_header] Unrecognised key: 7L Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: @7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "' Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: "L Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: 7H Step #5: [W::cram_decode_compression_header] Unrecognised key: U7 Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: E] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: V] Step #5: [W::cram_decode_compression_header] Unrecognised key: 7M Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: ' Step #5: [W::cram_decode_compression_header] Unrecognised key: I\ Step #5: [W::cram_decode_compression_header] Unrecognised key: /I Step #5: [W::cram_decode_compression_header] Unrecognised key: /I Step #5: [W::cram_decode_compression_header] Unrecognised key: '! Step #5: [W::cram_decode_compression_header] Unrecognised key: !4 Step #5: [W::cram_decode_compression_header] Unrecognised key: B9 Step #5: [W::cram_decode_compression_header] Unrecognised key: 'U Step #5: [W::cram_decode_compression_header] Unrecognised key: 7S Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: ]- Step #5: [W::cram_decode_compression_header] Unrecognised key: LT Step #5: [W::cram_decode_compression_header] Unrecognised key: LB Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: L" Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: V Step #5: [W::cram_decode_compression_header] Unrecognised key: "M Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: I7 Step #5: [W::cram_decode_compression_header] Unrecognised key: JL Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: UB Step #5: [W::cram_decode_compression_header] Unrecognised key: 'I Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: =3 Step #5: [W::cram_decode_compression_header] Unrecognised key: ,A Step #5: [W::cram_decode_compression_header] Unrecognised key: UC Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: "] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: :! Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "= Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: 6 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: 9 Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: $" Step #5: [W::cram_decode_compression_header] Unrecognised key: "6 Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: =3 Step #5: [W::cram_decode_compression_header] Unrecognised key: ,A Step #5: [W::cram_decode_compression_header] Unrecognised key: UC Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: "] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: :! Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "= Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: 6 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: 9 Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: $" Step #5: [W::cram_decode_compression_header] Unrecognised key: "6 Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: =3 Step #5: [W::cram_decode_compression_header] Unrecognised key: ,A Step #5: [W::cram_decode_compression_header] Unrecognised key: UC Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: "] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: :! Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised key: A7 Step #5: [W::cram_decode_compression_header] Unrecognised key: "= Step #5: [W::cram_decode_compression_header] Unrecognised key: U\ Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: 6 Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: BU Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: 9 Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: $" Step #5: [W::cram_decode_compression_header] Unrecognised key: "6 Step #5: [E::cram_huffman_decode_init] Malformed huffman header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: =3 Step #5: [W::cram_decode_compression_header] Unrecognised key: ,A Step #5: [W::cram_decode_compression_header] Unrecognised key: UC Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: IF Step #5: [W::cram_decode_compression_header] Unrecognised key: )I Step #5: [W::cram_decode_compression_header] Unrecognised key: I? Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: FM Step #5: [W::cram_decode_compression_header] Unrecognised key: I? Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: OI Step #5: [W::cram_decode_compression_header] Unrecognised key: CC Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: = Step #5: [W::cram_decode_compression_header] Unrecognised key: &) Step #5: [W::cram_decode_compression_header] Unrecognised key: &) Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: F0 Step #5: [W::cram_decode_compression_header] Unrecognised key: IF Step #5: [W::cram_decode_compression_header] Unrecognised key: C: Step #5: [W::cram_decode_compression_header] Unrecognised key: F> Step #5: [W::cram_decode_compression_header] Unrecognised key: !C Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: IC Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: T] Step #5: [W::cram_decode_compression_header] Unrecognised key: IT Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: IO Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: O Step #5: [W::cram_decode_compression_header] Unrecognised key: O Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: I, Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: T= Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key: O< Step #5: [W::cram_decode_compression_header] Unrecognised key: H) Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: !G Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: =U Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: =3 Step #5: [W::cram_decode_compression_header] Unrecognised key: ,A Step #5: [W::cram_decode_compression_header] Unrecognised key: UC Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: IF Step #5: [W::cram_decode_compression_header] Unrecognised key: )I Step #5: [W::cram_decode_compression_header] Unrecognised key: I? Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: FM Step #5: [W::cram_decode_compression_header] Unrecognised key: I? Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: OI Step #5: [W::cram_decode_compression_header] Unrecognised key: CC Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: = Step #5: [W::cram_decode_compression_header] Unrecognised key: &) Step #5: [W::cram_decode_compression_header] Unrecognised key: &) Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: F0 Step #5: [W::cram_decode_compression_header] Unrecognised key: IF Step #5: [W::cram_decode_compression_header] Unrecognised key: C: Step #5: [W::cram_decode_compression_header] Unrecognised key: F> Step #5: [W::cram_decode_compression_header] Unrecognised key: !C Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: IC Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: T] Step #5: [W::cram_decode_compression_header] Unrecognised key: IT Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: IO Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: O Step #5: [W::cram_decode_compression_header] Unrecognised key: O Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: I, Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: T= Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key: O< Step #5: [W::cram_decode_compression_header] Unrecognised key: H) Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: !G Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: =U Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: =3 Step #5: [W::cram_decode_compression_header] Unrecognised key: ,A Step #5: [W::cram_decode_compression_header] Unrecognised key: UC Step #5: [W::cram_decode_compression_header] Unrecognised key: I Step #5: [W::cram_decode_compression_header] Unrecognised key: H Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: IF Step #5: [W::cram_decode_compression_header] Unrecognised key: )I Step #5: [W::cram_decode_compression_header] Unrecognised key: I? Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: FM Step #5: [W::cram_decode_compression_header] Unrecognised key: I? Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: OI Step #5: [W::cram_decode_compression_header] Unrecognised key: CC Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: = Step #5: [W::cram_decode_compression_header] Unrecognised key: &) Step #5: [W::cram_decode_compression_header] Unrecognised key: &) Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::cram_decode_compression_header] Unrecognised key: & Step #5: [W::cram_decode_compression_header] Unrecognised key: F0 Step #5: [W::cram_decode_compression_header] Unrecognised key: IF Step #5: [W::cram_decode_compression_header] Unrecognised key: C: Step #5: [W::cram_decode_compression_header] Unrecognised key: F> Step #5: [W::cram_decode_compression_header] Unrecognised key: !C Step #5: [W::cram_decode_compression_header] Unrecognised key: T Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: IC Step #5: [W::cram_decode_compression_header] Unrecognised key: ) Step #5: [W::cram_decode_compression_header] Unrecognised key: T] Step #5: [W::cram_decode_compression_header] Unrecognised key: IT Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: IO Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: O Step #5: [W::cram_decode_compression_header] Unrecognised key: O Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: I, Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: T= Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key: &= Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 4 Step #5: [W::cram_decode_compression_header] Unrecognised key: O< Step #5: [W::cram_decode_compression_header] Unrecognised key: H) Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: TI Step #5: [W::cram_decode_compression_header] Unrecognised key: !G Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: H$ Step #5: [W::cram_decode_compression_header] Unrecognised key: =U Step #5: [W::cram_decode_compression_header] Unrecognised key: &B Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 8447 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8447 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 8447 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=>%ga%%_217922a%0a%0A>%d%0a%0ÿ744073709558446744073709551616A>%ga%%_O%18446Oa%0%_fqi>O%A0O%d%32°69a%0,>,>z_:O%0a%_O%184' is too large Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8535>K\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8535>K\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=%d" at byte offset 714 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%d%smÿ_O" at byte offset 736 Step #5: [E::fai_build_core] The last entry '%d%smÿ' has no sequence at line 56 Step #5: [E::refs_load_fai] Failed to open reference file 'data:aaIN*O:aÚ:,>z_:O%0a%_OO%0A>%d%0a%0z>z_:O%0a%_O%0A>%d%fqi0a%%_8O%0a%>z_:O%0a%_OO%0A>%d%0a%0,>z_:O%0a%_O%0A>%dÿCRACÿ@0`0@#ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ%fqi1a%%_:O%0a%_OO%0A>%d????????????0a%_OOÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ%0A>%d??????????????????0A>%d%0a%%:aÚ:,>z_:O%0a%_OO%0A>%d%4a%0,>z_:O%0a%_O%0A>%d%fqi0a%%_8O%0a%>z_:O%0a%_OO%0A>%d00%%a,>z_:O%0a%_O%0A>%;%fqi0a%%_:O%0a%_OO%0A>%d???????????????0A>%d%0a%%_O%0A0a%0a%0A>%d%smÿ_O%0A0a%0a%0A>%d%smÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ%0A>%d?????????ÿÿÿÿÿÿÿÿ?????????0A>ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ%h%0a%%:aÚ:,>z_:O%0a%_OO%0A>%dd%0a%0,>z_:O%0a%_O%0A>%d%fqi0a%%_8O%0a%>z_:O%0a%_OO%0A>%ÿÿÿÿÿÿÿ,z_:O%0a%_O%0A>%d%fqi0a%%_:O%0a%_OO%0A>%d????????????0a%_OO%0A>%d??????????????????0A>%d%0a%%_O%0A0a%0a%0A>%d%smÿ_O%0A0a%0a%0A>%d%smÿ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\x05\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "\xFF\x05\xFF\xFF\xFF\xFF\xFF\xFF\x"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #4/5 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: s3:*daat:ÿa%_:O%0ad%%äddõÛ¦¦¦¦¦¦¦¦ ¦¦¦¦¦¦¦¦¦¦¦¦{dddda%%dddccO%0a,>:_:O%0ccccccßcccc¦¦~¦¦ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÙ7ÕÕÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_Z!œœœœœœœÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_œœÿ?ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ”ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ0%0a%0: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*daat:ÿa%_:O%0ad%%äddõÛ¦¦¦¦¦¦¦¦ ¦¦¦¦¦¦¦¦¦¦¦¦{dddda%%dddccO%0a,>:_:O%0ccccccßcccc¦¦~¦¦ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÙ7ÕÕÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_Z!œœœœœœœÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_œœÿ?ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ”ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ0%0a%0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3:*daat:ÿa%_:O%0ad%%äddõÛ¦¦¦¦¦¦¦¦ ¦¦¦¦¦¦¦¦¦¦¦¦{dddda%%dddccO%0a,>:_:O%0ccccccßcccc¦¦~¦¦ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÙ7ÕÕÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_Z!œœœœœœœÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_œœÿ?ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ”ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ0%0a%0: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3:*daat:ÿa%_:O%0ad%%äddõÛ¦¦¦¦¦¦¦¦ ¦¦¦¦¦¦¦¦¦¦¦¦{dddda%%dddccO%0a,>:_:O%0ccccccßcccc¦¦~¦¦ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÙ7ÕÕÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_Z!œœœœœœœÕÕÅÕÕÕÕÕÕÕÕ1@ºÕ_œœÿ?ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ”ÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔÔ0%0a%0' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 962 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 962 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 962 Step #5: #128 pulse exec/s: 16 rss: 446Mb Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [E::fai_build3_core] Failed to open the file data:aa:aŠ : Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'data:aa:aŠ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [E::fai_build3_core] Failed to open the file data:aa:aŠ : Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'data:aa:aŠ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #4/5 Step #5: [E::fai_build3_core] Failed to open the file data:aa:aŠ : Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 'data:aa:aŠ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::cram_encode_container] Keeping non-ref mode from now on Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 967 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 967 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 967 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [E::process_one_read] Unknown CIGAR op code 9 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxx:::::::::::::::::::::::::::::' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxx:::::::::::::::::::::::::::::" Step #5: [W::vcf_parse_info] INFO ':*:::ú:::::::::::::Ž:::::::::::::::::`::::::::::::::::::::::::::::::::::::::::::‡‡‡c‡‡‡‡‡‡‡‡Ü@CO' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ":*:::ú:::::::::::::Ž:::::::::::::::::`::::::::::::::::::::::::::::::::::::::::::‡‡‡c‡‡‡‡‡‡‡‡Ü@CO" Step #5: [W::vcf_parse_format_dict2] FORMAT '‡‡‡‡‡‡‡‡~‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡/‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxxx|‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "‡‡‡‡‡‡‡‡~‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡/‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxxx|‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Åÿÿÿÿÿÿûÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Åÿÿÿÿÿÿûÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'º' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "º" Step #5: [W::vcf_parse_format_dict2] FORMAT '®' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "®" Step #5: [W::vcf_parse_format_dict2] FORMAT '1' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "1" Step #5: [W::vcf_parse_format_dict2] FORMAT '##idx##' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "##idx##" Step #5: [W::vcf_parse_format_dict2] FORMAT '&' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "&" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ó €¥' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ó €¥" Step #5: [W::vcf_parse_format_dict2] FORMAT '#' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "#" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_info] INFO '‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxx:::::::::::::::::::::::::::::' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxx:::::::::::::::::::::::::::::" Step #5: [W::vcf_parse_info] INFO ':*:::ú:::::::::::::Ž:::::::::::::::::`::::::::::::::::::::::::::::::::::::::::::‡‡‡c‡‡‡‡‡‡‡‡Ü@CO' is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: ":*:::ú:::::::::::::Ž:::::::::::::::::`::::::::::::::::::::::::::::::::::::::::::‡‡‡c‡‡‡‡‡‡‡‡Ü@CO" Step #5: [W::vcf_parse_format_dict2] FORMAT '‡‡‡‡‡‡‡‡~‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡/‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxxx|‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "‡‡‡‡‡‡‡‡~‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡/‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡yxxxxxx|‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡‡" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'Åÿÿÿÿÿÿûÿ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "Åÿÿÿÿÿÿûÿ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'º' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "º" Step #5: [W::vcf_parse_format_dict2] FORMAT '®' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "®" Step #5: [W::vcf_parse_format_dict2] FORMAT '1' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "1" Step #5: [W::vcf_parse_format_dict2] FORMAT '##idx##' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "##idx##" Step #5: [W::vcf_parse_format_dict2] FORMAT '&' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "&" Step #5: [W::vcf_parse_format_dict2] FORMAT 'ó €¥' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "ó €¥" Step #5: [W::vcf_parse_format_dict2] FORMAT '#' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "#" Step #5: [E::bcf_write] Unchecked error (67 Contig not defined in header,Tag not defined in header,Invalid tag) at :0 Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ?T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ?T Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: @B Step #5: [W::cram_decode_compression_header] Unrecognised key: DJ Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: BP Step #5: [W::cram_decode_compression_header] Unrecognised key: P? Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: $" Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: PZ Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: "B Step #5: [W::cram_decode_compression_header] Unrecognised key: $D Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: 9@ Step #5: [W::cram_decode_compression_header] Unrecognised key: $$ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: S Step #5: [W::cram_decode_compression_header] Unrecognised key: S Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 77 Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: B" Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: >$ Step #5: [W::cram_decode_compression_header] Unrecognised key: ! Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: BC Step #5: [W::cram_decode_compression_header] Unrecognised key: B5 Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: M Step #5: [W::cram_decode_compression_header] Unrecognised key: AT Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Z Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: >B Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: P$ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: /, Step #5: [W::cram_decode_compression_header] Unrecognised key: &? Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 3 Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: ?D Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ?T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ?T Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: @B Step #5: [W::cram_decode_compression_header] Unrecognised key: DJ Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: BP Step #5: [W::cram_decode_compression_header] Unrecognised key: P? Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: $" Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: PZ Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: "B Step #5: [W::cram_decode_compression_header] Unrecognised key: $D Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: 9@ Step #5: [W::cram_decode_compression_header] Unrecognised key: $$ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: S Step #5: [W::cram_decode_compression_header] Unrecognised key: S Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 77 Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: B" Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: >$ Step #5: [W::cram_decode_compression_header] Unrecognised key: ! Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: BC Step #5: [W::cram_decode_compression_header] Unrecognised key: B5 Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: M Step #5: [W::cram_decode_compression_header] Unrecognised key: AT Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Z Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: >B Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: P$ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: /, Step #5: [W::cram_decode_compression_header] Unrecognised key: &? Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 3 Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: ?D Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ?T Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key ?T Step #5: [W::cram_decode_compression_header] Unrecognised key: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: @B Step #5: [W::cram_decode_compression_header] Unrecognised key: DJ Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: E Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key: > Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: BP Step #5: [W::cram_decode_compression_header] Unrecognised key: P? Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: $" Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: PZ Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: "B Step #5: [W::cram_decode_compression_header] Unrecognised key: $D Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: 9@ Step #5: [W::cram_decode_compression_header] Unrecognised key: $$ Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: S Step #5: [W::cram_decode_compression_header] Unrecognised key: S Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 77 Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: B" Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: >$ Step #5: [W::cram_decode_compression_header] Unrecognised key: ! Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: "" Step #5: [W::cram_decode_compression_header] Unrecognised key: D$ Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: BC Step #5: [W::cram_decode_compression_header] Unrecognised key: B5 Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: M Step #5: [W::cram_decode_compression_header] Unrecognised key: AT Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Z Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: ? Step #5: [W::cram_decode_compression_header] Unrecognised key: , Step #5: [W::cram_decode_compression_header] Unrecognised key: >B Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: P$ Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: /, Step #5: [W::cram_decode_compression_header] Unrecognised key: &? Step #5: [W::cram_decode_compression_header] Unrecognised key: A Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: 3 Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: 7 Step #5: [W::cram_decode_compression_header] Unrecognised key: @ Step #5: [W::cram_decode_compression_header] Unrecognised key: ?D Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $ Step #5: [W::cram_decode_compression_header] Unrecognised key: @" Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_format1_append] Corrupted aux data for read 0* flag 0 Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_aux] Unknown sub-type 'A' for aux type 'B' Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 976 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 976 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 976 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: s3: Ù&&::::::::::::::‬.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&::::::::::::::‬.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3: Ù&&::::::::::::::‬.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&::::::::::::::‬.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #4/5 Step #5: s3: Ù&&::::::::::::::‬.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&::::::::::::::‬.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Keeping non-ref mode from now on Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 977 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 977 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 977 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=filefo\x9C\x9C\x9C\x9C\x9C\x9C\x9C\x9C" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##>filefo\x9C\x9C\x9C\x9C\x9C\x9C\x9C\x9C" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 988 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 988 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 988 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 988 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 988 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 988 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 989 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 989 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 989 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build3_core] Failed to open the file +++++++++++++++++++@SQ : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file '+++++++++++++++++++@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [E::fai_build3_core] Failed to open the file +++++++++++++++++++@SQ : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file '+++++++++++++++++++@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [E::fai_build3_core] Failed to open the file +++++++++++++++++++@SQ : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file '+++++++++++++++++++@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name "27Dz11."; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 9 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] The last entry ':::::_%O%%~%ú%O%%iM¤%aiM::?%%a%%fq…::¹::*::_:_:%aiM::?%®a::ÿÿÿÿÿÿÿP::_:%aiM::?%ªi::_%O%BZhfa%O%f?//@SQ' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@:::::_%O%%~%%fa%O%%iM¤%aiM::?%%a%%fq…::¹::*::_:_:%aiM::?%%aea::ÿÿÿÿÿÿÿP::_:%aiM::?%%aai::_%O%BZhfa%O%f?//@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [E::fai_build_core] The last entry ':::::_%O%%~%ú%O%%iM¤%aiM::?%%a%%fq…::¹::*::_:_:%aiM::?%®a::ÿÿÿÿÿÿÿP::_:%aiM::?%ªi::_%O%BZhfa%O%f?//@SQ' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@:::::_%O%%~%%fa%O%%iM¤%aiM::?%%a%%fq…::¹::*::_:_:%aiM::?%%aea::ÿÿÿÿÿÿÿP::_:%aiM::?%%aai::_%O%BZhfa%O%f?//@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 11 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: [E::fai_build_core] The last entry ':::::_%O%%~%ú%O%%iM¤%aiM::?%%a%%fq…::¹::*::_:_:%aiM::?%®a::ÿÿÿÿÿÿÿP::_:%aiM::?%ªi::_%O%BZhfa%O%f?//@SQ' has no sequence at line 1 Step #5: [E::refs_load_fai] Failed to open reference file 'data:,@:::::_%O%%~%%fa%O%%iM¤%aiM::?%%a%%fq…::¹::*::_:_:%aiM::?%%aea::ÿÿÿÿÿÿÿP::_:%aiM::?%%aai::_%O%BZhfa%O%f?//@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 998 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 998 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 998 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 1002 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 1002 Step #5: [E::inflate_gzip_block] Gzip file truncated Step #5: [E::bgzf_read_block] Reading GZIP stream failed at offset 1002 Step #5: [E::bam_set1] Query name too long Step #5: [E::bam_set1] Query name too long Step #5: [E::bam_set1] Query name too long Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: 8" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: U8 Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: "+ Step #5: [W::cram_decode_compression_header] Unrecognised key: D+ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: B* Step #5: [W::cram_decode_compression_header] Unrecognised key: P* Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: 8" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: U8 Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: "+ Step #5: [W::cram_decode_compression_header] Unrecognised key: D+ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: B* Step #5: [W::cram_decode_compression_header] Unrecognised key: P* Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: 8" Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: U8 Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: "+ Step #5: [W::cram_decode_compression_header] Unrecognised key: D+ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: M Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: 5 Step #5: [W::cram_decode_compression_header] Unrecognised key: L Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: &" Step #5: [W::cram_decode_compression_header] Unrecognised key: B* Step #5: [W::cram_decode_compression_header] Unrecognised key: P* Step #5: [E::cram_gamma_decode_init] Malformed gamma header stream Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=K\xC8\xC0\xC9\xCA\x1A:M\xE5\xFF\xFF\xFF\xFF\x07\xDDW\xFF\xFF)\xFD3\xFF\xFF\xFFXO\x17\r\xF7\xB3\xB1\xC5\x96\xF5\xBF\xACQ\tSN:A\xFF/\x012H\xB7hr\x9B\x99\x90\x8D\x92\x9E!\x02\xC4#\x01DVC\xF3\xA0\x80\xA2" Step #5: [W::bcf_hdr_parse_line] Incomplete header line, trying to proceed anyway: Step #5: [##INFO=>S*&>@N000000000******************************ÏÕ*****************òÙÕÕÕ****,,,,,,,,,,,,,,,,,,,,,,$,,,-,,,,,,,,,,,,,,,*ÏÕ************““““““““““““““““““““““““““““““““““““““““““““““““““““““““““,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,M::mem_pestat,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ÊÓÓÓÓÓÓÓ,>>S*&>@N000000000******************************ÏÕ*****************òÙÕÕÕ****,,,,,,,,ñ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,$,,,-,,,,,,,,,,,,,,,,,,,,2147483650cB@,,,,,,,,,,,,,,,,,,,,,,,,,,N:@ûûûûûûûûûûûûûû\,,,,,,,,,,,,,,Ø,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Ô'ÓÓÓÓÓÝ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,=VCF6aaaaaaaaT$1655" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "@W,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,(,,,,,,,,$,,,-,,,,,,,,,,,,,,,,,,,,2147483648cB@,,,ÔÓÓÓÓÓÓÖ,,,,/,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,M::mem_pestat,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ÊÓÓÓÓÓÓÓ,>>S*&>@N000000000******************************ÏÕ*****************òÙÕÕÕ****,,,,,,,,,,,,,,,,,,,,,,$,,,-,,,,,,,,,,,,,,,*ÏÕ************““““““““““““““““““““““““““““““““““““““““““““““““““““““““““,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,M::mem_pestat,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ÊÓÓÓÓÓÓÓ,>>S*&>@N000000000******************************ÏÕ*****************òÙÕÕÕ****,,,,,,,,ñ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,$,,,-,,,,,,,,,,,,,,,,,,,,2147483650cB@,,,,,,,,,,,,,,,,,,,,,,,,,,N:@ûûûûûûûûûûûûûû\,,,,,,,,,,,,,,Ø,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Ô'ÓÓÓÓÓÝ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,=VCF6aaaaaaaaT$1655" with no LN: tag Step #5: [E::sam_hrecs_update_hashes] Header includes @SQ line "@W,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,(,,,,,,,,$,,,-,,,,,,,,,,,,,,,,,,,,2147483648cB@,,,ÔÓÓÓÓÓÓÖ,,,,/,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,M::mem_pestat,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ÊÓÓÓÓÓÓÓ,>>S*&>@N000000000******************************ÏÕ*****************òÙÕÕÕ****,,,,,,,,,,,,,,,,,,,,,,$,,,-,,,,,,,,,,,,,,,*ÏÕ************““““““““““““““““““““““““““““““““““““““““““““““““““““““““““,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,M::mem_pestat,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ÊÓÓÓÓÓÓÓ,>>S*&>@N000000000******************************ÏÕ*****************òÙÕÕÕ****,,,,,,,,ñ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,$,,,-,,,,,,,,,,,,,,,,,,,,2147483650cB@,,,,,,,,,,,,,,,,,,,,,,,,,,N:@ûûûûûûûûûûûûûû\,,,,,,,,,,,,,,Ø,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Ô'ÓÓÓÓÓÝ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,=VCF6aaaaaaaaT$1655" with no LN: tag Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 4 (MMMMMMMMMMMMMMMXMMMMMMMMMMMMMMMMMMM) Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 4 (MMMMMMMMMMMMMMMXMMMMMMMMMMMMMMMMMMM) Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [E::fai_build_core] Format error, carriage return not followed by new line at line 6 Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>zS:O%0a%_O%0A>$d%0a%0a%0d%0a%0d%0Ã@%?%0a%0,>z_:O%0a%]a%0d%0a%0d0a%0,,>z_@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] CIGAR length invalid at position 4 (MMMMMMMMMMMMMMMXMMMMMMMMMMMMMMMMMMM) Step #5: [W::sam_read1_sam] Parse error at line 6 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: [E::fai_build_core] Format error, carriage return not followed by new line at line 6 Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>zS:O%0a%_O%0A>$d%0a%0a%0d%0a%0d%0Ã@%?%0a%0,>z_:O%0a%]a%0d%0a%0d0a%0,,>z_@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: s3://///////////////////////////////////////////////////////////////////////////////////////////////////////////@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3://///////////////////////////////////////////////////////////////////////////////////////////////////////////@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [E::parse_cigar] Unrecognized CIGAR operator Step #5: [W::sam_read1_sam] Parse error at line 8 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3://///////////////////////////////////////////////////////////////////////////////////////////////////////////@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3://///////////////////////////////////////////////////////////////////////////////////////////////////////////@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: s3: Ù&&.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #1/5 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #2/5 Step #5: s3: Ù&&.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #3/5 Step #5: s3: Ù&&.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 12 Step #5: [W::cram_encode_container] Retrying embed_ref=2 mode for #4/5 Step #5: s3: Ù&&.@SQ: Invalid argument Step #5: [E::refs_load_fai] Failed to open reference file 's3: Ù&&.@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_encode_container] Failed to find reference, switching to non-ref mode Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::cram_encode_slice_header] Reference position too large for CRAM 3 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::sam_format1_append] Corrupted aux data for read flag 128 Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [E::bam_read1] CIGAR and query sequence lengths differ for Step #5: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [E::bam_read1] CIGAR and query sequence lengths differ for Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 9600 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 9600 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 9600 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [E::bam_aux_next] Corrupted aux data for read flag 128 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 40 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 80 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 125 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 131 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%ÿÿÿÿO%0}A>$dÛÆa" at byte offset 162 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 181 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 211 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%ÿÿÿÿO%0}A>$dÛÆa" at byte offset 284 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "$dÛÆa" at byte offset 297 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 303 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 313 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 333 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%ÿÿÿÿO%0}A>$daÆ%0Ûa" at byte offset 369 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "$dÛÆa" at byte offset 378 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 384 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 394 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 416 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 422 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 477 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 483 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%ÿÿÿÿO%0}A>$dÛÆa" at byte offset 514 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "0a" at byte offset 524 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "" at byte offset 528 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "$dÛÆa" at byte offset 556 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 562 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 572 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%?" at byte offset 611 Step #5: [W::fai_insert_index] Ignoring duplicate sequence "%$" at byte offset 621 Step #5: [E::fai_build3_core] Failed to open FASTA index data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$daÆ%0Ûa%0d%0a%0d%0A>$dÛÆ0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$daÆ%0Ûa%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿ%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%O%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0´aÛÆa%0a%0a%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>z.fai : Read-only file system Step #5: [E::refs_load_fai] Failed to open reference file 'data:aÚ:,>z_:O%0a%_OOa%_ÿÿA>$dÛÆa%0a%0d%0A>%?%0AÛÆa%0a%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$daÆ%0Ûa%0d%0a%0d%0A>$dÛÆ0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0%0d%0A>%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$daÆ%0Ûa%0d%0a%0d%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿ%?%0a%0,>zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$?%0a%0a%0d%0A>%0a%0d%0A>%?%0a%0,zaa%0d%0%0a%0d%0A>%ÿÿÿÿO%0}A>$dÛÆa%0a%d00%0da%%0A>0a%0a%0d%0A>%0a%0d%O%0}A>$dÛÆa%0a%d00%0da%%0A>$dÛÆa%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>zaa%0d%0%0a%0d%0A>%?%0a%0a%0d%0A>%?%0´aÛÆa%0a%0a%0a%0d%0A>%?%0aÛÆa%0a%0d%0A>%$%0a%0,>z' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized mate reference name ""; treated as unmapped Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P0 Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: P$ Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: J Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: K Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P@ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: J Step #5: [W::cram_decode_compression_header] Unrecognised key: @P Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: WP Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: P0 Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: D1 Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 4" Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $R Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: UJ Step #5: [W::cram_decode_compression_header] Unrecognised key: 0L Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P0 Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: P$ Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: J Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: K Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P@ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: J Step #5: [W::cram_decode_compression_header] Unrecognised key: @P Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: WP Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: P0 Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: D1 Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 4" Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $R Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: UJ Step #5: [W::cram_decode_compression_header] Unrecognised key: 0L Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key B" Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised preservation map key \ Step #5: [W::cram_decode_compression_header] Unrecognised key: U Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P0 Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: P$ Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: J Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: K Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P@ Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: J Step #5: [W::cram_decode_compression_header] Unrecognised key: @P Step #5: [W::cram_decode_compression_header] Unrecognised key: # Step #5: [W::cram_decode_compression_header] Unrecognised key: WP Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: D" Step #5: [W::cram_decode_compression_header] Unrecognised key: P0 Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: ]H Step #5: [W::cram_decode_compression_header] Unrecognised key: 0 Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: \ Step #5: [W::cram_decode_compression_header] Unrecognised key: . Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: D1 Step #5: [W::cram_decode_compression_header] Unrecognised key: DB Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: 1 Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key: D Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: B Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: C Step #5: [W::cram_decode_compression_header] Unrecognised key: " Step #5: [W::cram_decode_compression_header] Unrecognised key: 4" Step #5: [W::cram_decode_compression_header] Unrecognised key: P Step #5: [W::cram_decode_compression_header] Unrecognised key: P" Step #5: [W::cram_decode_compression_header] Unrecognised key: ] Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: Step #5: [W::cram_decode_compression_header] Unrecognised key: $R Step #5: [W::cram_decode_compression_header] Unrecognised key: H" Step #5: [W::cram_decode_compression_header] Unrecognised key:  Step #5: [W::cram_decode_compression_header] Unrecognised key: F Step #5: [W::cram_decode_compression_header] Unrecognised key: UJ Step #5: [W::cram_decode_compression_header] Unrecognised key: 0L Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 20 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 20 Step #5: [E::fai_build3_core] Failed to open the file f@SQ : No such file or directory Step #5: [E::refs_load_fai] Failed to open reference file 'f@SQ' Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_read1_sam] Parse error at line 20 Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 16 Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 16 Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_read1_sam] Parse error at line 16 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 25 Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [E::bam_write1] Positional data is too large for BAM format Step #5: [W::sam_hdr_sanitise] Unexpected NUL character in header. Possibly truncated Step #5: [W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated Step #5: [W::cram_get_ref] Failed to populate reference "" Step #5: [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions Step #5: [W::cram_write_SAM_hdr] No M5 tags present and could not find reference Step #5: [W::cram_write_SAM_hdr] Enabling embed_ref=2 option Step #5: [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::bam_tag2cigar] encodes a CIGAR with 1 operators at the CG tag Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [E::sam_parse_B_vals_r] Numeric value in B array out of allowed range Step #5: [W::sam_read1_sam] Parse error at line 25 Step #5: [E::cram_generate_reference] Cannot build reference with unsorted data Step #5: [W::cram_encode_container] Failed to build reference, switching to non-ref mode Step #5: [E::cram_encoder_init] Unable to initialise codec of type BETA Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'hZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'GT' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT 'Z' at :0 is not defined in the header, assuming Type=String Step #5: [W::vcf_parse_format_dict2] FORMAT '' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "" Step #5: [W::vcf_parse_format_dict2] FORMAT 'gT' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.) Step #5: [W::bcf_hrec_check] Invalid contig name: "" Step #5: [W::vcf_parse_filter] FILTER '' is not defined in the header Step #5: [W::vcf_parse_format_dict2] FORMAT 'èZ' at :0 is not defined in the header, assuming Type=String Step #5: [W::bcf_hrec_check] Invalid tag name: "èZ" Step #5: [W::vcf_parse_format_dict2] FORMAT 'G' at :0 is not defined in the header, assuming Type=String Step #5: [E::bcf_write] Unchecked error (3 Contig not defined in header,Tag not defined in header) at :0 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6##idx##9w23173781630371BA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6##idx##9w23173781630371BABA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi##idx##6:923173781630371BA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6##idx##9w23173781630371BA" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6:923173781630371BA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6##idx##9w23173781630371BA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6##idx##9w23173781630371BABA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi##idx##6:923173781630371BA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6##idx##9w23173781630371BA" Step #5: [E::bcf_hdr_parse_line] Could not parse the header line: "##flefi6:923173781630371BA" Step #5: [W::bcf_get_version] Couldn't get VCF version, considering as 4.2 Step #5: [W::bcf_hdr_parse] Could not parse header line: "#" Step #5: [E::bcf_hdr_parse] Could not parse the header, sample line not found Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name "85\x1D,665\xA738,,65531S,654385\x1"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ":"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",M::bwa_idx_load_from_disk,,,,,,,,"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ":"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ",,,,,,,,,,,,,,,,,,,,41553S,655385\"...; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped Step #5: [W::sam_parse1] empty query name Step #5: [W::sam_parse1] unrecognized reference name ":"; treated as unmapped Step #5: [W::sam_parse1] mapped mate cannot have zero coordinate; treated as unm