Unified Genotyper and Recalibrator errors

Good day again. I have repeatedly been picking up errors when running either the SNP/Indel Unified Genotyper and VariantRecalibrator tools.

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: Unable to parse header with error: /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub5214228717936515167.tmp (Too many open files), for input source: /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub5214228717936515167.tmp
ERROR ------------------------------------------------------------------------------------------

As I am a student I am not sure if this is a command problem or whether it is administrative. Has anyone come across this problem before?

Best Answer


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