gatk requests enormous amounts of memory. How to limit it?

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23 months ago

optimistsso4co3 ▴ 110

I'm trying to call variants but node crashes every time. It gas 512GB ram, 128 cores and i send qsub job requesting 16 cores and 64 GB for each genome. So in total around 7 genomes are computed at the same time there.

How to make sure node does not crash?

gatk • 592 views

ADD COMMENT • link updated 23 months ago by brunobsouzaa ▴ 830 • written 23 months ago by optimistsso4co3 ▴ 110

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If you are using a job scheduler then nodes should not crash. I assume your job is getting killed because it is running out of resources? It may help to actually provide the exact tool you are using/command line you are using.

ADD REPLY • link 23 months ago by GenoMax 141k

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how do you invoke gatk ?

ADD REPLY • link 23 months ago by Pierre Lindenbaum 161k

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Can you plz post your code to call GATK?

ADD REPLY • link 23 months ago by brunobsouzaa ▴ 830

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