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GATK temporary directory

trickytanktrickytank The Walter and Eliza Hall Institute of Medical Research. Melbourne, AustraliaPosts: 3Member
edited October 2012 in Ask the GATK team

Hello,

During running of the depthOfCoverage tool, I get the error:
/tmp/RsQHCt1W: No space left on device

I have tried changing the TMPDIR environment variable (and exporting) but eventually I get the same error. Is there a way to change the temporary directory that GATK uses?

I'm running GATK v2.1-8-g5efb575 on a Linux system.

Thanks,
Rick

Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,469Administrator, Dev admin
    Answer ✓

    That's not specific to GATK, I believe you should be able to specify it on the command line with something like this:

    java -Djava.io.tmpdir=/tmp ...  
    

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,469Administrator, Dev admin
    Answer ✓

    That's not specific to GATK, I believe you should be able to specify it on the command line with something like this:

    java -Djava.io.tmpdir=/tmp ...  
    

    Geraldine Van der Auwera, PhD

  • trickytanktrickytank The Walter and Eliza Hall Institute of Medical Research. Melbourne, AustraliaPosts: 3Member

    Thanks for your help. :)

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