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Error: Unified Genotyper:Null alleles are not supported

navonil13navonil13 Member
edited January 2014 in Ask the GATK team
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: Null alleles are not supported
at org.broadinstitute.variant.variantcontext.Allele.(Allele.java:117)
at org.broadinstitute.sting.utils.haplotype.Haplotype.(Haplotype.java:61)
at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.trimHaplotypes(PairHMMIndelErrorModel.java:235)
at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeGeneralReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:438)
at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeDiploidReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:251)
at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:149)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:331)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:232)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
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: Null alleles are not supported
ERROR ------------------------------------------------------------------------------------------

Command was:java -jar GenomeAnalysisTK-2.8-1/GenomeAnalysisTK.jar -R ref/humhg19.fa -T UnifiedGenotyper -I 9.bam_recal_RG.bam --dbsnp dbsnp_135.hg19.vcf -o 9.bam_WG_snp_indel.raw.vcf -stand_call_conf 0.0 -stand_emit_conf 0.0 -glm BOTH -U ALLOW_N_CIGAR_READS

Post edited by navonil13 on

Best Answers

Answers

  • navonil13navonil13 Member

    I have tried with latest nightly and the error still persists
    INFO 20:50:31,795 GATKRunReport - Uploaded run statistics report to AWS S3

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

    java.lang.IllegalArgumentException: Null alleles are not supported
    at org.broadinstitute.variant.variantcontext.Allele.(Allele.java:120)
    at org.broadinstitute.sting.utils.haplotype.Haplotype.(Haplotype.java:61)
    at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.trimHaplotypes(PairHMMIndelErrorModel.java:235)
    at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeGeneralReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:438)
    at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeDiploidReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:251)
    at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:149)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:331)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:232)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version nightly-2014-01-10-ga785cf2):
    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: Null alleles are not supported
    ERROR ------------------------------------------------------------------------------------------
  • navonil13navonil13 Member

    Any update on bthis bur?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @navonil13,

    Yes, we have a proposed fix for the bug; now we just need to do a little more testing and put it through code review before we can make the fix available. Should take another day or two at most.

  • navonil13navonil13 Member

    with 3 samples it worked (16th's nightly).. with rest the variant calling is in progress. Thank you so very much.

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