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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Queue + Torque: keep_completed required?
I'm running Queue 3.1 with Torque 4.2.8. I found that with Torque's default setup Queue reported spurious failures for tasks running on remote nodes but not the local node (my "cluster" has the pbs_server node doing compute as well).
The jobs in question would report FunctionEdge - Error:
but then print an apparently-successful GATK log file.
I found that after using qmgr to set queue queue_name keep_completed = 300 then the jobs successfully complete. However, considering that the job running on the local node always succeeded even without keep_completed set, I suspect I'm doing something obvious wrong, either with Torque or Queue, since I'm pretty new to both systems.
In particular I'm unsure which paths are expected to live in a node-private filesystem and which in a shared filesystem. I currently run my tasks from a shared scratch directory (yielding -Djava.io.tmpdir=/shared-scratch/.queue/tmp); is this correct? By contrast I note that for some reason /home/myuser/.drmaa/jobid.started and .exitcode files are being created, despite the fact that pbs_mom is running as root, which seems wrong.
Has anyone seen similar behaviour that could shed some light on the situation?