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exited with return code 247 on TCGA bam from drs:// url

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7 comments

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    Samantha Velasquez

    Hi breardon,

     

    Thanks for reaching out. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
    2. Click Save.

     

    Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

     

    Best,

    Samantha

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    breardon

    Hi Samantha,

    Oops, thank you - I had forgotten to do that. The workspace is vanallen-firecloud-nih/TCGA-KIRP-MOAlmanac and relevant submission ids are 7fefd0ed-049a-4bfb-9f00-529ccbec8891 and 96435592-7eb3-4606-bc86-2e2d10b253b8

     

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    breardon

    Just following up on this. Thank you! 

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    Samantha Velasquez

    Hi breardon,

     

    Sorry for the delay. We are still investigating issue and will get back to you as soon as we can.

     

    Best,

    Samantha

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    Samantha Velasquez

    Hi breardon,

     

    We think the issue here may be that you are not providing enough memory to the SamToFastq task, which is why it's failing. This value should be at least as much as the memory being allocated to the command (150GB), but it looks like you only have it set to 16GB. Can you try resubmitting the workflow with increased memory?

     

    Best,

    Samantha

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    breardon

    And that is why using WDLs written by other people can be dangerous. Thank you, Samantha! Shouldn't this have returned a PAPI error code 9 though, since the issue was memory? Why was this error code returned? 

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    Samantha Velasquez

    Hi breardon,

     

    Most likely, the command itself failed to allocate proper memory inside the VM and exited by itself instead of PAPI terminating the job.

     

    Best,

    Samantha

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