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Error executing process > 'ingress_tumor:checkBamHeaders (1)' #29

Closed Manoswini-02 closed 4 months ago

Manoswini-02 commented 5 months ago

Ask away!

I'm attempting to execute wf-somatic-variation on the cluster, but it's throwing an error: "Error executing process > 'ingress_tumor (1)'". As the error code suggests no BGZF EOF marker; file may be truncated, I verified the BAM files using samtools, and they appeared to be intact. I am using the same bam files for other analysis (wf-human-variation) and it worked. The data carries modified based calling for both 5mC 5hmC.

What am I missing? Do I need to look for read group information?

Below is the command: nextflow run epi2me-labs/wf-somatic-variation --bam_normal /lustre/project/skim5/MD/ONT_bam/P2_BAM/ --bam_tumor /lustre/project/skim5/MD/ONT_bam/P28_BAM/ --ref /lustre/project/skim5/MD/ONT_bam/hg38.fa --sv --snv --mod --sample_name P2_P28 --normal_min_coverage 0 --tumor_min_coverage 0 -profile singularity

Related log output

ERROR ~ Error executing process > 'ingress_tumor:checkBamHeaders (1)'

Caused by: Process ingress_tumor:checkBamHeaders (1) terminated with an error exit status (1)

Command executed:

workflow-glue check_bam_headers_in_dir input_dir > env.vars source env.vars DS_RUNIDS=$(workflow-glue get_ds_records --xam input_dir --key runid --cardinality zero-or-more --sep ',') DS_BASECALL_MODELS=$(workflow-glue get_ds_records --xam input_dir --key basecall_model --cardinality zero-or-one --sep ',' --explode_obviously)

Command exit status: 1

Command output: (empty)

Command error: [12:23:07 - workflow_glue] Bootstrapping CLI. [12:23:07 - workflow_glue] Starting entrypoint. Traceback (most recent call last): File "/home/mdash/.nextflow/assets/epi2me-labs/wf-somatic-variation/bin/workflow-glue", line 7, in cli() File "/home/mdash/.nextflow/assets/epi2me-labs/wf-somatic-variation/bin/workflow_glue/init.py", line 82, in cli args.func(args) File "/home/mdash/.nextflow/assets/epi2me-labs/wf-somatic-variation/bin/workflow_glue/check_bam_headers_in_dir.py", line 31, in main with pysam.AlignmentFile(xam_file, check_sq=False) as f: File "pysam/libcalignmentfile.pyx", line 748, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 958, in pysam.libcalignmentfile.AlignmentFile._open File "pysam/libchtslib.pyx", line 361, in pysam.libchtslib.HTSFile.checktruncation OSError: no BGZF EOF marker; file may be truncated

Manoswini-02 commented 4 months ago

To update, I was hunting down an error related to something I found in other tools, which hinted at removing the old BAM files. For me, the program started working (it's still running) when I separated it from the other BAM files in the folder, including the sorted ones.

Thanks!