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

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 • 294 views
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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.

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how do you invoke gatk ?

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Can you plz post your code to call GATK?

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