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Is the parallelism documentation for DepthOfCoverage correct?

LeeTL1220LeeTL1220 Jamaica Plain, MAPosts: 18Member, Broadie, Cancer Tools Developer

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html
states (bold is my emphasis):

Parallelism options

This tool can be run in multi-threaded mode using this option.

TreeReducible (-nt)

Yet when I run the GATK with -nt, I get an error that -nt is not supported (truncated to save space):

ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
ERROR MESSAGE: Invalid command line: Argument nt has a bad value: The analysis DepthOfCoverage aggregates results by interval. Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution. Please run your analysis without the -nt option.

Answers

  • LeeTL1220LeeTL1220 Jamaica Plain, MAPosts: 18Member, Broadie, Cancer Tools Developer

    Apologies for the poor markdown

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,566Administrator, GATK Developer admin

    No worries. We'll improve the error message on this for the next version; the issue is that by default, the tool produces a summary of data aggregated over intervals, which is not compatible with multithreading. However, if you disable the per-interval reporting (see -omitIntervalStatistics ifI remember correctly), you will be able to use the multithreading.

    Geraldine Van der Auwera, PhD

  • LeeTL1220LeeTL1220 Jamaica Plain, MAPosts: 18Member, Broadie, Cancer Tools Developer

    --omitIntervalStatistics got rid of the error. Thanks!

  • Shrey_SShrey_S Posts: 20Member
    edited January 2014

    So, what is the max memory that could be allocated to depthOfCoverage
    I use -Xmx2G.....I use the older GATK version GenomeAnalysisTK-1.6-13, hence cannot use multithreading option, i,.e -nt
    But if I go more that 2G on the -Xmx value then I think it wont make any difference..correct?

    Post edited by Shrey_S on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,566Administrator, GATK Developer admin

    Hi @Shrey_S,

    I would say that's correct, yes -- I wouldn't expect memory to be the limiting factor for DepthOfCoverage, so increasing the allocation won't make it go faster, unfortunately.

    Geraldine Van der Auwera, PhD

  • Shrey_SShrey_S Posts: 20Member

    So that means if I use -Xmx6G it would still use 2G which is the max it could use...
    Is 2G the standard max memory for all the GATK tools (i.e. if we run them without multithreading)?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,566Administrator, GATK Developer admin

    No, I mean you can allocate more, and if it needs to it could potentially use the extra memory (there is no hard limit set internally for any tool), but it is unlikely that the tool would need that much memory.

    Geraldine Van der Auwera, PhD

  • Shrey_SShrey_S Posts: 20Member
    edited January 2014

    Alright Geraldine..Thanks for the reply....:)

    Post edited by Shrey_S on
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