HaplotypeCaller raises an error with -A BaseCountsBySample

Hi GATK team , FYI I'm getting the following error with GATK 3.7:

<br />java  -X  -jar GenomeAnalysisTK.jar -T HaplotypeCaller    -R human_g1k_v37.fasta     --validation_strictness LENIENT    -I  .bam.list \
 -o "out.vcf.gz"  -l INFO         -nct 10 --dbsnp "138.b37.vcf"   --annotation PossibleDeNovo   --annotation AS_FisherStrand   --annotation AlleleBalance   --annotation AlleleBalanceBySample   --annotation BaseCountsBySample   --annotation GCContent   --annotation ClippingRankSumTest   --pedigree in.ped -L:BED "in.bed"

##### ERROR stack trace
java.lang.IllegalStateException: Never found start -1 or stop -1 given cigar 100I
        at org.broadinstitute.gatk.utils.sam.AlignmentUtils.getBasesCoveringRefInterval(AlignmentUtils.java:204)
        at org.broadinstitute.gatk.utils.sam.AlignmentUtils.countBasesAtPileupPosition(AlignmentUtils.java:1418)
        at org.broadinstitute.gatk.tools.walkers.annotator.BaseCountsBySample.getBaseCounts(BaseCountsBySample.java:135)
        at org.broadinstitute.gatk.tools.walkers.annotator.BaseCountsBySample.annotate(BaseCountsBySample.java:113)
        at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateGenotypes(VariantAnnotatorEngine.java:517)
        at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:278)
        at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:260)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.annotateCall(HaplotypeCallerGenotypingEngine.java:328)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:290)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:962)
        at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:250)
        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$ReadMapReduceJob.run(NanoScheduler.java:471)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

searching for '100I': the following command returns nothing:

find wordir -name "**.bam"   | while read F; do samtools view  $F "12:132806991-133841896" | grep 100I ; done

removing 'BaseCountsBySample' seems to fix the problem.

P.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @lindenb
    Hi P,

    I cannot reproduce the error message using --annotation PossibleDeNovo --annotation AS_FisherStrand --annotation AlleleBalance --annotation AlleleBalanceBySample --annotation BaseCountsBySample --annotation GCContent --annotation ClippingRankSumTest on some test data. Can you confirm this occurs when you don't use -nct 10? Please also try validating your BAM files with ValidateSamFile.

    -Sheila

  • Hi,
    I am getting the same error for a small subset of samples (~50 / 1000). This runs without the --annotation BaseCountsBySample, but I would really like to keep it if possible. It is happening with both GATKv3.7 and GATKv3.8. My command is:

    java  -X  -jar GenomeAnalysisTK.jar -T HaplotypeCaller  -R Pfalciparum.fasta -I bams.list -o gatk.vcf.gz --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 --max_alternate_alleles 6 --annotation BaseCountsBySample 
    

    Error:

    ##### ERROR stack trace 
    java.lang.IllegalStateException: Never found start -1 or stop -1 given cigar 12I
            at org.broadinstitute.gatk.utils.sam.AlignmentUtils.getBasesCoveringRefInterval(AlignmentUtils.java:204)
            at org.broadinstitute.gatk.utils.sam.AlignmentUtils.countBasesAtPileupPosition(AlignmentUtils.java:1418)
            at org.broadinstitute.gatk.tools.walkers.annotator.BaseCountsBySample.getBaseCounts(BaseCountsBySample.java:135)
            at org.broadinstitute.gatk.tools.walkers.annotator.BaseCountsBySample.annotate(BaseCountsBySample.java:113)
            at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateGenotypes(VariantAnnotatorEngine.java:517)
            at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:278)
            at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:260)
            at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.annotateCall(HaplotypeCallerGenotypingEngine.java:328)
            at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:290)
            at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:970)
            at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:252)
            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:98)
            at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
            at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
            at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):
    ##### 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://software.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Never found start -1 or stop -1 given cigar 12I
    ##### ERROR ------------------------------------------------------------------------------------------
    

    Thanks!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @ellenelle
    Hi,

    You cannot run GVCF mode on multiple BAM files. You can only produce one GVCF per input BAM file. Have a look at this article.

    -Sheila

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