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Old 04-09-2013, 08:05 AM   #1
opulcy97
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Location: moon

Join Date: Nov 2012
Posts: 19
Default 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
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Old 04-09-2013, 08:52 AM   #2
mastal
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Location: uk

Join Date: Mar 2009
Posts: 667
Default

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
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Old 04-09-2013, 05:55 PM   #3
vdauwera
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Location: Boston, MA

Join Date: Apr 2012
Posts: 43
Lightbulb

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.
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Old 04-12-2013, 02:24 AM   #4
opulcy97
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Location: moon

Join Date: Nov 2012
Posts: 19
Default

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