HaplotypeCaller Error on some bam files

bigeybigey Montpellier, FranceMember
edited October 2016 in Ask the GATK team

Hello GATK team,

I report an error using HaplotypCaller on 3 bam files (other 34 bam files were processed without problem)

Exemple:

$ nohup /opt/java/jre1.8.0_102/bin/java -jar /opt/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/bigey/Bakery/RefGenome/SACE_s288c_all_chromosomes_numeric_2011-05-16.fasta -I ../BaseQualityRecalibration/BTE.BaseQualityRecalibration.bam --emitRefConfidence GVCF -o BTE.raw.snps.indels.g.vcf >BTE.HaplotypeCaller.log 2>&1 &

See the error message below.

Any idea to overcome this problem?

Fred

Error message for HaplotypeCaller:

INFO  11:52:21,584 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  11:52:21,588 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29 
INFO  11:52:21,588 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  11:52:21,588 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk 
INFO  11:52:21,588 HelpFormatter - [Mon Oct 10 11:52:21 CEST 2016] Executing on Linux 3.2.0-110-generic amd64 
INFO  11:52:21,589 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14 JdkDeflater 
INFO  11:52:21,595 HelpFormatter - Program Args: -T HaplotypeCaller -R /home/bigey/Bakery/RefGenome/SACE_s288c_all_chromosomes_numeric_2011-05-16.fasta -I ../BaseQualityRecalibration/BTE.BaseQualityRecalibration.bam --emitRefConfidence GVCF -o BTE.raw.snps.indels.g.vcf 
INFO  11:52:21,599 HelpFormatter - Executing as bigey@spo-pi-isis on Linux 3.2.0-110-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_102-b14. 
INFO  11:52:21,600 HelpFormatter - Date/Time: 2016/10/10 11:52:21 

../..

##### ERROR --
##### ERROR stack trace 
java.util.NoSuchElementException
    at java.util.HashMap$HashIterator.nextNode(HashMap.java:1439)
    at java.util.HashMap$KeyIterator.next(HashMap.java:1461)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.reduceNumberOfAlternativeAllelesBasedOnLikelihoods(HaplotypeCallerGenotypingEngine.java:336)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:264)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:964)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:251)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
    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.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
##### 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 https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR ------------------------------------------------------------------------------------------
Post edited by bigey on

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