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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.
GATK Queue GridEngine Job submission slows dramatically over time
I'm using Queue 3.4 with a Univa GridEngine cluster. Everything runs fine, and at first the time between job submissions is only a few seconds. But the rate at which queue submits jobs to the cluster slows to a crawl - up to 40 seconds per job after a few hundred submissions, and slowly increasing. Any idea what might be happening here? With a scatterCount of 1000, it can take a full day just to submit all jobs to the cluster for a HaplotypeCaller run.