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GATK Queue ./.queue/ directory translated to an absolute path? All jobs fail on SGE.

WimSWimS Member Posts: 27

When trying to run the Haplotype caller using GATK Queue all my jobs failed because they couldn't write to the tmp files in the ./.queue directory.

This seems to be related to the working directory from which the Queue command is started, and the ./.queue directory is created.

The head node of the SGE grid I want to use and from where I start the Queue is server8.

When I start the Queue command on that server the working directory is translated from a path that is accessible from everywhere on the SGE cluster to a path that is only accessible locally.

Example working directory: /home/sge_share_sever8/variantCalling is translated to the absolute path /data/variantCalling which is only accesible locally.

If I start the Queue from a working directory that is mounted from another server everything workes fine.

Example working directory: /home/sge_share_sever12/variantCalling stays /home/sge_share_sever12/variantCalling and everything works fine.

Is it a bug or feature that the ./.queue directory is translated from a normal path to an absolute path?

Or can I specify another location for the ./.queue directory that will not be translated to an absolute path.

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,727 admin

    Hi there,

    Unfortunately we're not able to provide support for Queue issues at the moment. The software is provided as is, and if you have issues due to system or network configurations it's up to you to get it to work. You may need to ask for help from your IT department. Good luck!

    Geraldine Van der Auwera, PhD

  • WimSWimS Member Posts: 27

    I am the local IT department. And also Java developer and bio-informatician :P

    Well I can understand that you can't look into everything and the problem might be at our side.
    It might also be at your side and be as easy as changing

    queueTmpDir.getAbsolutePath()

    http://docs.oracle.com/javase/6/docs/api/java/io/File.html#getAbsolutePath()

    to

    queueTmpDir.getPath();

    http://docs.oracle.com/javase/6/docs/api/java/io/File.html#getPath()

    when creating the commands that will be executed for every data chunk.

    For the time being we'll just use a workaround by starting the Queue from a working directory on another server.

    @Geraldine_VdAuwera said:
    Hi there,

    Unfortunately we're not able to provide support for Queue issues at the moment. The software is provided as is, and if you have issues due to system or network configurations it's up to you to get it to work. You may need to ask for help from your IT department. Good luck!

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