PairHMM Log Probability cannot be greater than 0 Error with HaplotypeCaller
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Dear All,

I've encountered the following error while processing one of the regions from an interval file that I want to re-discover/genotype with the HC. Note that I've processed the other 4.2mln regions without any problems. A quick search on the forum did not lead to any results. Let me know if you'd like more information!

Command:

~/tools/jdk1.7.0_25/bin/java -Xmx8g \ -jar ~/tools/GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -L ~/gonl/projects/SV/ug/gonl.union_pindel_ug_clever.sites.2.vcf.gz \ -L 1:237759920-238000001 \ -nct 6 \ -isr INTERSECTION \ -o ~/results/trio-analysis/hc/1_237759920-238000001.vcf \ -R /target/gpfs2/gcc/resources/hg19/indices/human_g1k_v37.fa \ -I ~/gonl/projects/trio-analysis/resources/bqsr2.bams.list \ -XL ~/gonl/projects/accessibleGenome/results/ALL.accessible.out.mask.intervals \ -minPruning 5 \ 2>&1 | tee /target/gpfs2/gcc/home/lfrancioli/logs/trio-analysis/hc/1_237759920-238000001.out

Error:

`##### ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.IllegalStateException: PairHMM Log Probability cannot be greater than 0: haplotype: [84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84], read: [84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84], result: 0.002992 at org.broadinstitute.sting.utils.pairhmm.PairHMM.computeReadLikelihoodGivenHaplotypeLog10(PairHMM.java:131) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeReadLikelihoods(LikelihoodCalculationEngine.java:262) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeReadLikelihoods(LikelihoodCalculationEngine.java:205) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:770) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:140) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
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: PairHMM Log Probability cannot be greater than 0: haplotype: [84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84], read: [84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84], result: 0.002992`
ERROR ------------------------------------------------------------------------------------------

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