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Germline CNV WDL - SIGKILL

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    Jason Cerrato

    Hi stanedav,

    Happy to see if we can help here. Do you have stdout and stderr files you can provide?

    Kind regards,

    Jason

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    stanedav

    Hi Jason, here is generated stdout stderr file:

    https://www.dropbox.com/s/tbwkk4d645bd6q4/stdout_stderr.txt?dl=0

    Command I run for generate this file:

    java -jar cromwell-50.jar run ./germline_CNV/cnv_germline_cohort_workflow.wdl --inputs ./germline_CNV/inputs_short.json &>stdout_stderr.txt

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    Jason Cerrato

    Hi stanedav,

    Thank you for providing the file. I see that since you've collected the stdout and stderr to a single file it's about as verbose as the log—I am essentially looking for a way to narrow down to where the actual issue is shown to be occurring.

    It looks like the issue is specifically occurring with the GermlineCNVCallerCohortMode task. It may take some time to dig into this issue, but I'll try to get back to you as soon as I can.

    Just to confirm, can you link me to where you downloaded the workflow?

    Kind regards,

    Jason

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    Jason Cerrato

    Hi stanedav,

    Do you still require any assistance with this? If so, can you link me to where you downloaded the workflow?

    Many thanks,

    Jason

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    stanedav

    Hi Jason, sorry for the late response. I downloaded the workflow here:

    https://github.com/broadinstitute/gatk/tree/master/scripts/cnv_wdl/germline

    (I used git to download whole GATK_master directory with scripts where I found the workflow.

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    stanedav

    Hello Jason, I would like to ask if you have any updates to my issue.

    Thank you very much.

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    Beri Shifaw

    Hi stanedav,

    Looks like your workflow is failing at the task GermlineCNVCallerCohortMode. The workflow log file you linked tells me the log messages at a high level, describing the status of each task but doesn't tell me what caused the shards for that task to fail. Those log messages should be found in each individual shard running for that task. 

    You maybe able to find it in the following directory: 

    ..

    <some local path>/cromwell-executions/CNVGermlineCohortWorkflow/71b72b96-8d7c-470f-8b35-3514af3a0ae7/call-GermlineCNVCallerCohortMode/shard-14/

    I'm using shard 14 as an example but any of the ones that failed should be fine. Please provide a link to this type of log file. 

    Something else to double check is the resource usage for the machine you are running the workflow on. While running the workflow make sure the memory and diskspace isn't approaching its limits. (e.g. `free -h` for memory and `df -h` for disk usage)

     

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    stanedav

    Hello Beri,

    here are the logs, you got point that there is a memory issue. How can I set a memory limit for the whole workflow? I have 64 GB RAM in my machine. 

     

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    Beri Shifaw

    Like you mentioned and from the log message from the stderr log below, you may need some additional memory for your input file. 

    The exit code indicates that the process was terminated. This may mean the process requires additional memory.

    There doesn't seem to be a variable to allow you to set the memory for the whole workflow but there are individuals variables for each task you can set. Currently the default java memory being used for the GermlineCNVCallerCohortMode task is 6.5 GB , you can increase this by adding the mem_gb_for_germline_cnv_caller input parameter to your input json file and setting the variable.

    "CNVGermlineCohortWorkflow.mem_gb_for_germline_cnv_caller": <add GB integer here>

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