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GATK run-time error

mikawinmikawin Member
edited October 2012 in Ask the GATK team


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 
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 -        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
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(
    at org.broadinstitute.sting.gatk.walkers.genotyper.PoolGenotypeLikelihoods.calculateACConformationAndUpdateQueue(
    at org.broadinstitute.sting.gatk.walkers.genotyper.PoolGenotypeLikelihoods.computeLikelihoods(
    at org.broadinstitute.sting.gatk.walkers.genotyper.PoolIndelGenotypeLikelihoods.add(
    at org.broadinstitute.sting.gatk.walkers.genotyper.PoolIndelGenotypeLikelihoods.add(
    at org.broadinstitute.sting.gatk.walkers.genotyper.PoolGenotypeLikelihoodsCalculationModel.getLikelihoods(
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(
##### 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
##### ERROR
##### ERROR ------------------------------------------------------------------------------------------


Best Answers


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    We had a few bugs with the pool-related arguments that have been fixed. Could you please upgrade to the latest version of GATK (2.1-11) and try again?

  • delangeldelangel Broad InstituteMember
    Accepted Answer

    Can you pls update to the latest version (2.1.x) and see if this still happens? Note that you'll have to drop the -pnrm POOL -glm POOLBOTH arguments

  • Hey guys,

    I can upgrade to the latest version. However, I am calling SNPs for a Haploid genome and in reply to another query posted in the forum, it is recommended that the POOLBOTH flag be turned on if sample ploidy != 2


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