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

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2.6 years ago

optimistsso4co3 ▴ 130

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 • 745 views

ADD COMMENT • link updated 2.6 years ago by brunobsouzaa ▴ 840 • written 2.6 years ago by optimistsso4co3 ▴ 130

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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 2.6 years ago by GenoMax 148k

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how do you invoke gatk ?

ADD REPLY • link 2.6 years ago by Pierre Lindenbaum 164k

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Can you plz post your code to call GATK?

ADD REPLY • link 2.6 years ago by brunobsouzaa ▴ 840

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