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Specifying jobRunner memory allocation

micknudsenmicknudsen DenmarkMember ✭✭

Hi,

I am trying to use GATK Queue to submit scatter-gather jobs on our local cluster. However, the jobs almost always run out of memory, because only 1GB is allocated by default. I run Queue with the

-jobRunner Drmaa

option, and I have tried all different combinations of

-memLimit 8
-resMemLimit 8
-resMemReq 8

to see if I could somehow force it to allocate more, but the problem persists.

Any ideas how to increase the memory allocation? Our cluster uses SLURM for job submission.

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