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GATK run-time error

mikawinmikawin Posts: 9Member
edited October 2012 in Ask the GATK team

Hello,

I am getting the following run-time error when I run the GATK UnfiedGenotyper to call SNPs. I have used the command as shown below successfully for 20+ samples, but got the error message for about 5 others.

What should I be doing differently?

INFO  09:24:43,209 HelpFormatter - --------------------------------------------------------------------------------- 
INFO 09:24:43,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.0-21-ga40b695, Compiled 2012/07/26 06:21:05
INFO 09:24:43,212 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:24:43,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:24:43,213 HelpFormatter - Program Args: -R MyRef.fasta -T UnifiedGenotyper -I aRef.rReads.indelRealigned.bam -dcov 10000 -A AlleleBalance -ploidy 1 -pnrm POOL -glm POOLBOTH -o aRef.rReads.unfilter.vcf
INFO 09:24:43,214 HelpFormatter - Date/Time: 2012/09/28 09:24:43
INFO 09:24:43,214 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:24:43,214 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:24:43,273 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:24:43,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 09:24:43,912 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
INFO 09:24:44,641 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
INFO 09:24:44,641 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 09:25:15,212 TraversalEngine - supercont2.1:56001 5.60e+04 30.7 s 9.1 m 0.3% 2.9 h 2.9 h
INFO 09:25:45,731 TraversalEngine - supercont2.1:83001 8.30e+04 61.2 s 12.3 m 0.4% 3.9 h 3.9 h
INFO 09:26:16,754 TraversalEngine - supercont2.1:117001 1.17e+05 92.3 s 13.1 m 0.6% 4.1 h 4.1 h
INFO 09:26:46,878 TraversalEngine - supercont2.1:138001 1.38e+05 2.0 m 14.8 m 0.7% 4.6 h 4.6 h
INFO 09:27:16,916 TraversalEngine - supercont2.1:178001 1.78e+05 2.5 m 14.3 m 0.9% 4.5 h 4.4 h
...
...
...
...
...
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INFO 12:21:17,972 TraversalEngine - supercont2.9:1116247 1.37e+07 2.9 h 12.9 m 72.7% 4.0 h 66.2 m
INFO 12:21:49,842 TraversalEngine - supercont2.9:1140247 1.37e+07 3.0 h 12.9 m 72.8% 4.1 h 66.0 m
INFO 12:22:20,139 TraversalEngine - supercont2.9:1186247 1.38e+07 3.0 h 12.9 m 73.1% 4.0 h 65.4 m
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 0
at org.broadinstitute.sting.gatk.walkers.genotyper.PoolIndelGenotypeLikelihoods.getLikelihoodOfConformation(PoolIndelGenotypeLikelihoods.java:198)
at org.broadinstitute.sting.gatk.walkers.genotyper.PoolGenotypeLikelihoods.calculateACConformationAndUpdateQueue(PoolGenotypeLikelihoods.java:553)
at org.broadinstitute.sting.gatk.walkers.genotyper.PoolGenotypeLikelihoods.computeLikelihoods(PoolGenotypeLikelihoods.java:512)
at org.broadinstitute.sting.gatk.walkers.genotyper.PoolIndelGenotypeLikelihoods.add(PoolIndelGenotypeLikelihoods.java:171)
at org.broadinstitute.sting.gatk.walkers.genotyper.PoolIndelGenotypeLikelihoods.add(PoolIndelGenotypeLikelihoods.java:65)
at org.broadinstitute.sting.gatk.walkers.genotyper.PoolGenotypeLikelihoodsCalculationModel.getLikelihoods(PoolGenotypeLikelihoodsCalculationModel.java:242)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:277)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:190)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:353)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:119)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:62)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.0-21-ga40b695):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: 0
##### ERROR ------------------------------------------------------------------------------------------

Thanks,
Mika

Post edited by Geraldine_VdAuwera on

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