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GATK Depth of Coverage randomly crashes?
Thank you for reading! I'm running GATK (v3.6-0-g89b7209) DepthofCoverage on a list of bam files. I originally had my files separated as a list of 23 paired bams for normal and tumor but I ran out of memory so I'm running them as 4 groups (Essentially N1, N2, T1, and T2).
While running, the first batch, N1, completed successfully without any errors and gave proper output files. T1 and N2 however just exited without providing a reason for the exit error in the output file. They both just stopped around 94% (Chr22 ~90 min left) and there's nothing else in the output.
Does this look like a system issue or a problem with one of my bam files that's throwing off the batch? I'm re-running the failed batches at the moment.
Thank you for your time!