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GATK:Unified Genotyper runtime error


I am using GATK unified genotyper for SNP and indel calling. My code is as follows:

$javaPath/java -Xmx4g -jar $gatkPath/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R $humanRefSequence \
-I "$sampleID".recal.bam \
-B:dbsnp,vcf $humanDbsnpFile \
-nt 8 -glm BOTH \
-stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 250 \
-l INFO \
-A AlleleBalance -A DepthOfCoverage -A FisherStrand \
-log "$sampleID".GATKvariants.log -o "$sampleID".GATKvariants.raw.vcf

However, after running few minutes it's showing the following error:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 1.0.5877):
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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR MESSAGE: Unable to create BasicFeatureReader using feature file , for input source: /tmp/org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub5104773249721434217.tmp
ERROR ------------------------------------------------------------------------------------------

I looked around and couldn't find a proper solution for it. I got stuck with for quite awhile. Can anyone please tell me what is the main reason for this error and how I can overcome it?

Many thanks in advance.


Best Answer


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