Hi there,
Today when I tried to perform Joint Genotyping by using GenomeAnalysisTK-3.4-46 with the parameters below, I got an error message like this:
**ERROR MESSAGE: Unable to parse header with error: /tmp/org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub6890620965177124656.tmp (Too many open files), for input source: /tmp/org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub6890620965177124656.tmp
ERROR MESSAGE: There was a failure because temporary file /tmp/org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub2577240191427705652.tmp could not be found while running the GATK with more than one thread. Possible causes for this problem include: your system's open file handle limit is too small, your output or temp directories do not have sufficient space, or just an isolated file system blip

**

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Argument variables passed in. User-modifiable parameters.

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VARIANT=
BUILD=hg19
VQSLOD=99.9
MEM=1000
PROC=64
READBACK=no
OUTPUT=

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Check and setup of the genome build file

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if [ "$BUILD" = "hg19" ]
then
REFERENCE=/hg19/ucsc.hg19.fasta
DBSNP=/SNPs/dbsnp_138.hg19.excluding_sites_after_129.vcf
INDEL_1KG=/indels/1000G_phase1.indels.hg19.sites.vcf
INDEL_MILLS=/indels/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
HAPMAP=/SNPs/hapmap_3.3.hg19.sites.vcf
OMNI=/SNPs/1000G_omni2.5.hg19.sites.vcf
SNP_1KG=/SNPs/1000G_phase1.snps.high_confidence.hg19.sites.vcf

I was not able to understand the exact problem, because the data were processed until chromosome 2 and after that the job gave an error and exited.

If you could help me to understand the underlying reason of the problem, I would be grateful.

Thank you.

Burcu