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run wld files in local cluster

jml96jml96 CambridgeMember

Hi,
I attended the GATK course in Cambridge (UK) and I am now adapting the 1-CNV_Somatic_Panel wdl files that I downloaded from github. I've changed cnv_common_tasks.wdl, cnv_somatic_panel_workflow.b37.inputs.json and cnv_somatic_panel_workflow.wdl to point out the directory to the bam files, reference and local gatk. When I run the following command in the server
java -jar .../cromwell-44.jar run .../cnv_somatic_panel_workflow.wdl --inputs .../gatk4-somatic-cnvs/cnv_somatic_panel_workflow.b37.inputs.json
I get the following error:
[2019-07-17 16:39:30,78] [error] WorkflowManagerActor Workflow bf30e28a-59cc-4f88-b969-02c020101526 failed (during ExecutingWorkflowState): Job CNVSomaticPanelWorkflow.PreprocessIntervals:NA:1 exited with return code -1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr.
Could not retrieve content: Could not read from /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr

I tried also to run it with singularity and I get exactly the same message.
Is somebody able to help me to solve this issue?
Thank you.

Regards,
João

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin

    @jml96 ,

    Happy that you are continuing with GATK after the workshop. The message above is indicating that there was an error with the workflow that you just ran
    Workflow bf30e28a-59cc-4f88-b969-02c020101526 failed (during ExecutingWorkflowState)
    and if you would like to know more check the the following file
    Check the content of stderr for potential additional information: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr.

    Please check the contents of the stderr file for a clearer error message from the workflow.

  • jml96jml96 CambridgeMember

    Hi,
    I saw this stderr error but didn't know either you to clear the error message.

    /usr/bin/docker-current: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?.
    See '/usr/bin/docker-current run --help'.
    cat: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/docker_cid: No such file or directory
    "docker wait" requires at least 1 argument(s).
    See 'docker wait --help'.

    Usage: docker wait CONTAINER [CONTAINER...]

    Block until one or more containers stop, then print their exit codes
    cat: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/docker_cid: No such file or directory
    "docker rm" requires at least 1 argument(s).
    See 'docker rm --help'.

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

    Remove one or more containers

    Could you help me now?

    Regards,
    João

  • bshifawbshifaw Member, Broadie, Moderator admin

    Looks like it's having trouble with docker.
    /usr/bin/docker-current: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?. See '/usr/bin/docker-current run --help'.

    Can you confirm docker is installed and running on your machine?
    Try

    sudo docker engine check
    docker ps
    
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