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error in GATK mitochondria pipeline

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    Samantha (she/her)

    Hi CenLiau

     

    Happy to take a closer look for you here. Do you mind sharing a link to access all the files associated with your job, either in a Google bucket or Google drive? You can give my email (svelasqu@broadinstitute.org) permission if you don't want the access to be public.

     

    Best,

    Samantha

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    Samantha (she/her)

    Hi CenLiau,

     

    Thanks for providing your WDL and json files. Can you also share the execution directory for the job so I can take a look at the .log and stderr files to see what went wrong? You can just upload the full execution directory to the same Google drive.

     

    Thanks,

    Samantha

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    CenLiau

    Hi Samantha,

    Thanks.

    This is the link to the execution folder

    https://drive.google.com/drive/folders/1pW93VkQw2oLhC29A4z_CniqtypJRqWCL?usp=sharing

     

    Cen

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    Beri

    Hi Cen,

    Do you have docker installed locally and tested that it works fine? The stderr background log shows it doesn't have access to the docker_cid file. This file would normally be found in the execution directory aswell, it contains a list of docker uuids used to run the workflow. 

    docker: Failed to create the container ID file: open /WORKSPACE/Cen/mtDNA/gatk_practice/cromwell-executions/MitochondriaPipeline/b60281de-ef22-4f07-a159-f3c6b4ff5d57/call-SubsetBamToChrM/execution/docker_cid: no such file or directory.
    See 'docker run --help'.
    cat: /WORKSPACE/Cen/mtDNA/gatk_practice/cromwell-executions/MitochondriaPipeline/b60281de-ef22-4f07-a159-f3c6b4ff5d57/call-SubsetBamToChrM/execution/docker_cid: No such file or directory
    "docker wait" requires at least 1 argument.
    See 'docker wait --help'.

    Usage: docker wait CONTAINER [CONTAINER...]

    Block until one or more containers stop, then print their exit codes
    cat: /WORKSPACE/Cen/mtDNA/gatk_practice/cromwell-executions/MitochondriaPipeline/b60281de-ef22-4f07-a159-f3c6b4ff5d57/call-SubsetBamToChrM/execution/docker_cid: No such file or directory
    "docker rm" requires at least 1 argument.
    See 'docker rm --help'.

    Usage: docker rm [OPTIONS] CONTAINER [CONTAINER...]

    Remove one or more containers

    For the cromwell-52 being used, was the jar installed directly or was it built from source? 

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    CenLiau

    Hi Beri,

    Thanks.

    Docker was installed in our local system. However, I don't have sudo access and didn't install docker locally in my own directory. I am sure, is that the problem?

    I downloaded cromwell-52.jar directly. 

     

    Thanks again,

    Cen

     

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    Beri

    Having Docker installed and functioning correctly is critical to running these workflows, so that might be the problem. Try testing if you can run docker yourself (helpful documentation)

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