UnifiedGenotyper crashes: HAPLOTYPE_MAX_LENGTH must be > 0 but got 0

Hello,

when I run the UnifiedGenotyper to call INDELs, I get the following error (detailed command line output below)
HAPLOTYPE_MAX_LENGTH must be > 0 but got 0

When I call only SNPs instead, it doe not occur. I have searched to find an answer to why this is happening, but cannot figure out the reason. Could this be a bug? I get the error no matter if I run the Realigner before or not.

Did you observe this problem before?

Command line output:
java -Xmx10g -jar ~/work/tools/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /media/rebecca/UUI/Work/BputSem/BputSem_gapfilled.final.fa -I realigned_A.bam -gt_mode DISCOVERY -glm INDEL -stand_call_conf 30 -stand_emit_conf 10 -o rawINDELS_q30_A.vcf -ploidy 10

INFO 15:50:47,987 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:50:47,990 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 15:50:47,990 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:50:47,990 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:50:47,996 HelpFormatter - Program Args: -T UnifiedGenotyper -R /media/rebecca/UUI/Work/BputSem/BputSem_gapfilled.final.fa -I realigned_A.bam -gt_mode DISCOVERY -glm INDEL -stand_call_conf 30 -stand_emit_conf 10 -o rawINDELS_q30_A.vcf -ploidy 10
INFO 15:50:48,002 HelpFormatter - Executing as rebecca@rebecca-ThinkPad-T440s on Linux 3.13.0-44-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32.
INFO 15:50:48,002 HelpFormatter - Date/Time: 2015/03/12 15:50:47
INFO 15:50:48,002 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:50:48,002 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:50:48,132 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:50:48,402 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 15:50:48,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:50:48,447 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
INFO 15:50:48,594 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 15:50:48,622 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:50:48,622 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:50:48,622 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:50:48,623 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 15:50:48,658 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 15:50:48,658 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
INFO 15:51:06,585 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: HAPLOTYPE_MAX_LENGTH must be > 0 but got 0
at org.broadinstitute.gatk.utils.pairhmm.PairHMM.initialize(PairHMM.java:97)
at org.broadinstitute.gatk.utils.pairhmm.N2MemoryPairHMM.initialize(N2MemoryPairHMM.java:60)
at org.broadinstitute.gatk.utils.pairhmm.LoglessPairHMM.initialize(LoglessPairHMM.java:66)
at org.broadinstitute.gatk.utils.pairhmm.PairHMM.computeLikelihoods(PairHMM.java:194)
at org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel.computeGeneralReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:461)
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyIndelGenotypeLikelihoods.add(GeneralPloidyIndelGenotypeLikelihoods.java:201)
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyIndelGenotypeLikelihoods.add(GeneralPloidyIndelGenotypeLikelihoods.java:124)
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoodsCalculationModel.getLikelihoods(GeneralPloidyGenotypeLikelihoodsCalculationModel.java:270)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoods(UnifiedGenotypingEngine.java:317)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:201)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:379)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:151)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, 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: HAPLOTYPE_MAX_LENGTH must be > 0 but got 0
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

Sign In or Register to comment.