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Unable to create temporary file for stub
I'm currently trying to run the Unified Genotyper on 99 whole-exome sampels however after ~12h I received the message:
ERROR MESSAGE: Failure working with the tmp directory /localscratch2/. Override with -Djava.io.tmpdir=X on the command line to a bigger/better file system. Exact error was Unable to create temporary file for stub: org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub
First I thought my tmp dir is too small, so I increased it to 4,4 TB. However, I received the same error after about 12h again (So it seems to be independent of the tmp dir size).
Do you have any suggestion what the problem could be ? Maybe the FileHandles ? (Although I did not see any error message complaining about the number of opened files.)
Thanks a lot!