Error running "gatk/mutect2-gatk4"
Thanks a lot for your helps. I'm almost finished this analysis.
When I run mutect2 on the normal-tumor pair, I encountered this error for call #50 of Mutect2.M2:
"htsjdk.samtools.FileTruncatedException: Premature end of file: /f4653fc5-f4a9-4f7e-ab53-1725b639043f/PairedEndSingleSampleWorkflow/e25a51f7-139d-40b7-8a5a-e8b5a2417ef1/call-GatherBamFiles/example_tumor.bam"
However, example_tumor.bam was generated by gatk/pre-processing-b37-gatk4, which was finished successfully. So I do not think this BAM file is truncated.
To make sure it is not a random GCP problem, I rerun mutect2. This time I got a similar but different error message at call #50 of Mutect2.M2:
"htsjdk.samtools.FileTruncatedException: Premature end of file: /27d5041a-60b4-4be2-b8e2-185547225d35/PairedEndSingleSampleWorkflow/08661c64-3b4b-44d1-a10d-8cd5e6dabf0a/call-GatherBamFiles/example_fibroblast.bam"
Again, I do not think "example_fibroblast.bam" is truncated.