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Are you experiencing PAPI error code 10? Read this for a workaround!

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    Brian Granger

    @Owen Wilkins, not a dumb question.

    maxRetries and preemptions are something you set on a task level, so it's something in the method, not the workspace. Specifically it's something that's specified in the runtime block of each task in your WDL(s) that comprise the method. You can see more about writing this into the WDL here: https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#maxretries

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    Rodrigo Guarischi-Sousa

    Hi

    I want to share my experience and save a lot of time, in case someone faces the same problem I had.

    I'm working with WGS samples from a NovaSeq 6000. I'm using the workflow 1-Processing-For-Variant-Discovery v1.1.0 from Broad's showcase workspace Germline-SNPs-Indels-GATK4-hg38. I struggled for dayyys trying to figure out why all my jobs were failing on the SortAndFixTags step with this poor "PAPI error code 10. The assigned worker has failed to complete the operation" message. 

    The exact same sample failed on slightly different step according to logs. Logs were suddenly interrupted without any informative error description, and this issue was driving me crazy. After digging deep into this and making tons of tests, I figure out the problem was a stupid out-of-memory problem. Simply increasing the default mem_size parameter on the workflow inputs from "7500 MB" to "10000 MB" totally solved the problem for me.

    This may be largely explained by my lack of previous experience with WDL and Terra, but I hope this tip helps other people and Broad to make Terra's logs more informative.

    Best, 

    Rodrigo Guarischi Sousa

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    Chatchawit Aporntewan

    Many thanks to Rodrigo Guarischi-Sousa. I am getting stuck at the same problem as yours. I have yearly experience running GATK workflows on my local server. However, on Terra now we cannot see all error messages such as out-of-memory error.

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