Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GenomeSTRiP CNVDiscovery error

0

7 comments

  • Avatar
    Thandeka

    Hi Bob the, -jobWrapper argument worked I am no longer getting errors, but the only problem I have now is that in the output directory there is nothing and when I open the log directory and read it there is nothing written on the run log files

    1
    Comment actions Permalink
  • Avatar
    Bhanu Gandham

    Hi Thandeka

    Tagging Bob Handsaker who will be able to help you out with your query. Thanks Bob!

    0
    Comment actions Permalink
  • Avatar
    Thandeka

    Hi, Bhanu thank you also thank you, Bob, in advance, I hope I will get the query sorted.

    0
    Comment actions Permalink
  • Avatar
    Bob Handsaker

    There is not a lot to go on in your description, but I will take a stab:

    I am assuming when you run SVDiscovery, that you are running on a cluster using Queue and a DRMAA binding and many parallel jobs and that this is running fine.

    One difference in the CNVDiscovery pipeline is that it does a recursive invocation of Queue. The first Queue process runs on the host where you execute the CNVDiscovery command (which must be a submission host, have the DRMAA library installed, etc.). In CNVDiscovery, some of the cluster jobs (generally one per chromosome) also run Queue to dispatch many other sub-jobs. This requires the execution host to also be a submission host and that you have the same DRMAA libraries and environment available on the execution hosts. For example, LD_LIBRARY_PATH must be set correctly. My guess is that the problem is something like this.

    If you are not already, note that you can use the -jobWrapperScript argument to Queue to allow you to inject a wrapper around each submitted job. This can be used to set environment variables, etc., on the execution host if necessary.

    0
    Comment actions Permalink
  • Avatar
    Thandeka

    Hi Bob, my apologies for writing something with missing information, yes i am running on a DRMAA on a cluster that uses SLURM. 

    This might be a tedious question but, what is the -jobWrapperScript argument? how do I write it on my script?

    Thank you for the reply

    0
    Comment actions Permalink
  • Avatar
    Bob Handsaker

    If you need to be able to control the execution environment of jobs running within Queue, one useful tool is the --jobWrapperScript argument to Queue. You use it like `-jobWrapperScript /path/to/my/wrapper.sh`.

    This will wrap the specified script around every command. You can use it to set special environment variables, load libraries, check exit status, etc.  A trivial example of wrapper.sh:

    #!/bin/bash
    echo "The wrapped cmd=$@"
    "$@" 2>&1

     

    0
    Comment actions Permalink
  • Avatar
    Thandeka

    Thank you very much Bob. Let me work on these suggestions and hopefully, it will work out.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk