To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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.