signal 11 (SEGV) (core dumped) issue
Hi,
I'm getting the following error message when running a workflow:
(ERR): bowtie2-align died with signal 11 (SEGV) (core dumped)
It seems like this error happens specifically on ubuntu (https://sourceforge.net/p/bowtie-bio/bugs/339/), although I was able to successfully run the docker on my local machine. Please let me know if you have any ideas as to how I can resolve the issue!
Please see this workflow for an example: https://job-manager.dsde-prod.broadinstitute.org/jobs/53c7ffa9-5842-40cd-9f8e-0bc2a5ee9896
Your team should already have access to the workspace (vanallen-firecloud-dfci/CR_NV_WES_IO_Meta).
Thanks for your help!
Comments
5 comments
Hi Daniel,
I'll take a look as soon as I am able and get back to you!
Kind regards,
Jason
Hi Daniel,
If this happens on ubuntu, would you be able to feed the task a non-ubuntu docker for the runtime?
https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#docker
Kind regards,
Jason
Hi Jason,
So I just tried running this on both centos and opensuse and still encountered the same issue. Is there something about terra that could be causing this to happen on this platform? I've seen some posts about this sort of thing happening on servers but not on local machines.
Thanks,
Daniel
Hi Daniel,
Hmm, it can be hard to tell without having more familiarity with Bowtie. Let me take a closer look to see if I can suss out what could be going on. Thank you for trying with the centos and opensuse runtimes.
Many thanks,
Jason
Would you be able to share this workflow with jcerrato@broadinstitute.org?
https://firecloud.terra.bio/#workspaces/vanallen-firecloud-dfci/CR_NV_WES_IO_Meta/workflows/hla-calling/phlat
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