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HaploytpeCaller ERROR MESSAGE: Event found on haplotype that wasn't added to priority list

When trying to run the HaplotypeCaller on specific indel sites with the -V and -allelesTrigger as shown below, I get the error stack trace at the bottom of this email. Any idea what might be happening?

Thanks!
Justin Zook

java -jar -Xmx22g ~/bioinfo/GenomeAnalysisTK-2.2-5-g3bf5e3f/GenomeAnalysisTK.jar -R /data/results/justin/GRCh37/human_g1k_v37.fasta -T HaplotypeCaller -I bam.bam -alleles:consensusall cons.vcf -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -stand_call_conf 0.0 -A AlleleBalance -A BaseQualityRankSumTest -A DepthOfCoverage -A FisherStrand -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZeroFraction -A MappingQualityZero -A QualByDepth -A ClippingRankSumTest -A RMSMappingQuality -o out.vcf -minPruning 3 -dcov 100 -allelesTrigger -dr 1000 -contamination 0.02 -L 1:1-249250621

I get the following stack trace:

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Event found on haplotype that wasn't added to priority list. Something went wrong in the merging of alleles.
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents(GenotypingEngine.java:269)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:423)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:104)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:249)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:204)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:179)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:136)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:29)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
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 2.2-5-g3bf5e3f):
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: Event found on haplotype that wasn't added to priority list. Something went wrong in the merging of alleles.
ERROR ------------------------------------------------------------------------------------------

Answers

  • ebanksebanks ✭✭✭✭ Broad InstituteMember, Broadie, Dev ✭✭✭✭

    Hi Justin,
    Thanks for reporting this. Would you mind uploading your BAM file and alleles VCF file to our ftp server so that I can take a look?
    Thanks!

  • jzookjzook Member

    Hi Eric,

    Thanks for the quick response. I've uploaded the alleles VCF file to your ftp server as Zook_indel_forcecalls.zip. The same error seems to occur with all bam files, including your group's NA12878 whole genome HiSeq bam on the 1000 Genomes technical site: http://www.ncbi.nlm.nih.gov/projects/faspftp/1000genomes/ftp/technical/working/20120117_ceu_trio_b37_decoy/. Let me know if you need any more information.

    Thanks,
    Justin

  • rpoplinrpoplin ✭✭✭ Member ✭✭✭

    Hi Justin,

    Thanks for the report and the files. We believe this is now fixed in the latest internal development version of the HaplotypeCaller and will be released with version 2.3 of the GATK-- which should be out next week.

    Cheers!

  • jzookjzook Member
    edited January 2013

    Thanks Ryan and Eric. It looks like I get a different error message now with version 2.3. Specifically I ran this:

    java -jar -Xmx22g  ~/bioinfo/GenomeAnalysisTK-2.3-2-g65db1dd/GenomeAnalysisTK.jar -R /data/results/justin/GRCh37/human_g1k_v37.fasta -T HaplotypeCaller -I 20120117_ceu_trio_b37_decoy/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.20120117.bam -alleles:consensusall OMNI_CG_1KG_SOL_ILL_454_HS_ILLCLIA_XIll_IllPCRFree_IonEx_XPSolWGLS_HapCallAll_conf2_mbq10_raw_merged_indelMNP_121205_1.vcf -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -stand_call_conf 0.0  -A AlleleBalance -A BaseQualityRankSumTest -A DepthOfCoverage -A FisherStrand -A HaplotypeScore -A HomopolymerRun -A MappingQualityRankSumTest -A MappingQualityZeroFraction -A MappingQualityZero -A QualByDepth -A ClippingRankSumTest -A RMSMappingQuality -o OMNI_CG_1KG_SOL_ILL_454_HS_ILLCLIA_XIll_IllPCRFree_IonEx_XPSolWGLS_HapCall_conf2_mbq10_raw_merged_IndelMNPvartrigger_121201_HSWGcall_1_givenallelesv2.3.vcf -minPruning 3 -dcov 100 -allelesTrigger -dr 1000 -contamination 0.02 -L 1:1-249250621
    

    and got the following error:

    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace 
    java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
            at java.util.ArrayList.RangeCheck(ArrayList.java:547)
            at java.util.ArrayList.get(ArrayList.java:322)
            at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.createAlleleMapper(GenotypingEngine.java:477)
            at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents(GenotypingEngine.java:133)
            at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:411)
            at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:107)
            at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:285)
            at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:230)
            at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:205)
            at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:131)
            at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:28)
            at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
            at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
            at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
            at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
            at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
            at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:94)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.3-2-g65db1dd):
    ##### 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: Index: 0, Size: 0
    ##### ERROR ------------------------------------------------------------------------------------------
    

    Thanks, and happy holidays!
    Justin

    Post edited by Geraldine_VdAuwera on
  • jzookjzook Member
    edited January 2013

    Since I left the last comment over the holidays, and at the same time as another comment, I wanted to make sure it wasn't lost. Have you had a chance to look at this issue?
    Thanks,
    Justin

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Hi Justin,

    No worries -- Ryan is looking at it.

  • rpoplinrpoplin ✭✭✭ Member ✭✭✭

    Hi Justin,

    Thanks for the report. This helped us identify a subtle but significant issue that we believe is now resolved in the latest internal development version of the HaplotypeCaller. Unfortunately in our development we somehow managed to delete the alleles archive that you uploaded. Would it be possible for you to re-upload the Zook_indel_forcecalls.zip file to our FTP?

    Thanks so much,

  • jzookjzook Member

    Hi Ryan,

    Thanks for working on this. I've uploaded the file Zook_indel_forcecalls.vcf.gz, which contains indels and MNPs like the one I uploaded before. I've also uploaded another file Zook_snpindel_forcecalls.vcf.gz, which contains SNPs and indels, so it forces assembly and calls at many more sites and gets the first error message above. Could you see if it works now as well?

    Thanks!
    Justin

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