Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Specifying jobRunner memory allocation
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
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.