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GermlineCNVCaller resource consumption #32

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HudoGriz opened this issue Oct 1, 2024 · 1 comment · Fixed by #38
Closed

GermlineCNVCaller resource consumption #32

HudoGriz opened this issue Oct 1, 2024 · 1 comment · Fixed by #38
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@HudoGriz
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HudoGriz commented Oct 1, 2024

Description of the bug

Hi,
I noticed that GermlineCNVCaller called in the GATK4_GERMLINECNVCALLER job eats up all available threads on a node. I made a quick fix by exporting MKL_NUM_THREADS & OMP_NUM_THREADS vars.

Kind regards,

Blaž

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@HudoGriz HudoGriz added the bug Something isn't working label Oct 1, 2024
@ramprasadn
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Good catch @HudoGriz. I will make the changes in the modules repo and then update them in the pipeline.

@ramprasadn ramprasadn mentioned this issue Nov 4, 2024
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@ramprasadn ramprasadn linked a pull request Nov 5, 2024 that will close this issue
update modules #38
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update modules nf-core/createpanelrefs
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@ramprasadn @HudoGriz