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.
Unable to determine status of job ID error
I occasionally get the following type of error when using genome strip CNVDisvovery pipeline on a cluster running SGE, it will run successfully for long periods of time and then arrive at this type of error
WARN 18:12:43,778 DrmaaJobRunner - Unable to determine status of job id 128098
1322 org.ggf.drmaa.DrmCommunicationException: failed receiving gdi request response for mid=63604 (can't send response for this message id - protocol error).
Usually I can just restart the pipeline and it will go to completion, but I don't know if I need to restart the whole stage? I have a hard time understanding sometimes whether there are actually problems I need to address. Any tips on troubleshooting this correctly?