Different pipelines getting return code 247 - Stops execution for no apparent reason

oskarvoskarv BergenMember

I've been running two pipelines on separate instances of cromwell version 30.1 and three times have the pipelines crashed with the return code 247. They're running entirely different tools so that's not a common element between them, and I frankly don't know where to begin since there's no useful error message, and I couldn't find anything on google about return code 247.
I found one search result on the forum here but there was no solution to the problem other than to use the latest gatk version at the time.

And I did nothing to fix it, I just restarted the pipeline and off it went, continuing as if nothing had happened? What could be causing this?

Answers

  • kshakirkshakir Broadie, Dev ✭✭

    Return code 247 doesn't mean anything specific to cromwell and may be specific to your task's command and the environment where the call is running.

    The first place to check would be the captured stderr and/or the stdout files for your failed call.

    If this return code 247 is happening intermittently it may require running the command by hand outside of cromwell. To get started reproducing the issue outside of cromwell one can also look closer at the commands generated by cromwell. Depending on the backend the script file may be called "exec.sh" or "script" and will be next to the stderr and stdout files.

  • mcovarrmcovarr Cambridge, MAMember, Broadie, Dev

    Users have had success getting around exit code 247s in GATK by increasing the default amount of memory that Docker gives to containers.

  • oskarvoskarv BergenMember

    @mcovarr said:
    Users have had success getting around exit code 247s in GATK by increasing the default amount of memory that Docker gives to containers.

    What is the default set to, and where do I change it?

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