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GATK Depth of Coverage randomly crashes?

vanish007vanish007 Cleveland, OHMember

Hi everyone,

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!


  • vanish007vanish007 Cleveland, OHMember

    Ok so a little more information. Linux gives an "ExitCode 1" around chr 22. Could this be some issue with the bam files or an argument?

    Here is my submitted command for one of my lists of bams:
    jdk1.8.0_73/bin/java -Xmx4g -jar GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T DepthOfCoverage -I Normal2.READS.bam.list -L Target.list -R Homo_sapiens_assembly19.fasta -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o Normal2.DATA

    Thank you very much!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I wonder if the tool is crashing on some super high depth sites. Can you try running on some small intervals on chromosome 22 to narrow down the issue?


  • vanish007vanish007 Cleveland, OHMember

    Thank you kindly for the response, Sheila. I'm still stuck and have been wondering if perhaps memory storage issues could be a culprit of this so I've cleared some space and am trying once more.

    Do you have any recommendations on how I can run small intervals on Chr 22? Thank you once again!



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Vai,

    You can use -L to test out small intervals. Have a look at this article for more help.


  • vanish007vanish007 Cleveland, OHMember

    Hi Sheila,

    Thank you for the article, I will try this out as well and update here once that is done. I appreciate the help very much!



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