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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.