Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

Slow in running Genome STRiP

I have such issue for a while, but I am not sure whether this is just the nature of the Genome STRiP software. In the preprocessing step, at first multiple small jobs will be submitted to the queue, but later, small jobs will be submitted one by one. The job log file shows that it only takes less than a minute to complete those later jobs (I think these jobs are just to index the bin files in the rccache folder), but the interval for java to submit these jobs ranges from 7 to 30 minutes. At first the interval is short, but later it becomes longer and longer. If I stopped the java at day 4, and restarted it, it will complete the preprocessing step a little faster due to shorten interval.
The genotyping step also behaves like that, which is very time consuming. Unfortunately, if I stopped the java and resubmit, unlike preprocessing or SVdiscovery, it will redo all the small jobs all over.
Is this normal?

Sign In or Register to comment.