Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller

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Blaz Vrhovsek

• June 30, 2022 11:27

I am trying to run the CNV pipeline as a snakemake workflow on a cluster, but DetermineGermlineContigPloidy and GermlineCNVCaller keep garbing all available cores.

XX:ParallelGCThreads=1 does nothing and --disableSpark does not exist. Even cpulimit seems unable to limit cores. I am guessing that the problem lies with the child python processes. Is there a way to limit them?

Much obliged,

Blaž

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  Anthony DiCi

  • July 05, 2022 17:13

  Hi Blaz Vrhovsek,

  Thank you for writing to the GATK Community Forum. We hope that we can adequately address your question.

  We would suggest that you try setting the following two environment variables to 1 and then re-running the tool.

  export MKL_NUM_THREADS=1
  export OMP_NUM_THREADS=1

  Let me know if that works.

  Best,

  Anthony

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