GATK:Unified Genotyper Error

opulcy97 · 04-09-2013, 08:05 AM

Hi,

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
##### 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
##### 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.

Regards,
Opulcy

mastal · 04-09-2013, 08:52 AM

the syntax for one of your parameters seems a bit unusual, is it a typo, or is it supposed to be that way?

-B:dbsnp,vcf

vdauwera · 04-09-2013, 05:55 PM

The syntax looks weird because that is a very old version, and the syntax has changed since. I strongly recommend you upgrade to a more recent version, Opulcy. The old version is buggy and slow; the newer version will be faster and give you much better results.

opulcy97 · 04-12-2013, 02:24 AM

Thanks for the tips. I have upgraded to the newer version. It's running fine now.

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04-09-2013, 08:05 AM	#1
opulcy97 Member Location: moon Join Date: Nov 2012 Posts: 19	GATK:Unified Genotyper Error Hi, 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 ##### 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 ##### 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. Regards, Opulcy

04-09-2013, 08:52 AM	#2
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 667	the syntax for one of your parameters seems a bit unusual, is it a typo, or is it supposed to be that way? -B:dbsnp,vcf

04-09-2013, 05:55 PM	#3
vdauwera Member Location: Boston, MA Join Date: Apr 2012 Posts: 43	The syntax looks weird because that is a very old version, and the syntax has changed since. I strongly recommend you upgrade to a more recent version, Opulcy. The old version is buggy and slow; the newer version will be faster and give you much better results.

04-12-2013, 02:24 AM	#4
opulcy97 Member Location: moon Join Date: Nov 2012 Posts: 19	Thanks for the tips. I have upgraded to the newer version. It's running fine now.