I'm trying to run your ExomeGermlineSingleSample workflow (Source: github.com/gatk-workflows/gatk4-exome-analysis-pipeline/ExomeGermlineSingleSample:update2.0v)
I was able to successfully use this workflow to analyze the sample dataset (SRR099969.unmapped.bam), as described in the documentation here.
When I try to analyze my own provided exome dataset, the first several steps of the analysis succeed, but the job fails during the BamProcessing.SortSam step. The workflow log contains the error message: "Job Failed with Error Code 10 for a machine where Preemptible is set to false". I have tried this two times using version 1.1 and a third time using version 2.0. These have all failed with Error Code 10 during SortSam. I have provided some more information here.
I would appreciate any advise you can give me to enable this workflow to succeed on my dataset.
Thanks in advance!
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