GATK 3.7 error message: not a strict subset of per read allele map alleles

sozkan123sozkan123 BarcelonaMember

I am trying to run GATK 3.7 for variant calling and I keep getting this error. Any comments about what this error is? Thanks!

ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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: VC alleles [A*, C, ] not a strict subset of per read allele map alleles []
ERROR ------------------------------------------------------------------------------------------

INFO 11:51:27,856 ProgressMeter - 1:12907532 9.48476025E8 2.5 m 0.0 s 0.9% 4.7 h 4.7 h
INFO 11:51:41,137 ProgressMeter - 1:10043261 4.51176908E8 60.0 s 0.0 s 0.6% 2.7 h 2.7 h
INFO 11:51:57,857 ProgressMeter - 1:16360411 1.354980846E9 3.0 m 0.0 s 1.1% 4.7 h 4.7 h
WARN 11:52:04,691 AnnotationUtils - Annotation will not be calculated, genotype is not called
WARN 11:52:04,735 AnnotationUtils - Annotation will not be calculated, genotype is not called

ERROR --
ERROR stack trace

java.lang.IllegalStateException: VC alleles [A, ATCT*, ] not a strict subset of per read allele map alleles []
at org.broadinstitute.gatk.utils.sam.AlignmentUtils.countBasesAtPileupPosition(AlignmentUtils.java:1408)
at org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts.getBaseCounts(BaseCounts.java:93)
at org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts.annotate(BaseCounts.java:78)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:315)
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.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:316)
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)

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sozkan123
    Hi,

    Can you please confirm this happens with the latest nightly build?

    Thanks,
    Sheila

  • sozkan123sozkan123 BarcelonaMember

    Hi,
    We are not sure if it is the latest nightly build, we are using GATK 3.7, downloaded in January this year, did you uploaded an updated version of GATK 3.7?
    Thanks for your quick reply
    Selen

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sozkan123
    Hi Selen,

    You can download the latest nightly build here.

    -Sheila

  • BWDavisBWDavis Bethesda, MDMember

    Hello Sheila,

    I too am getting this error across numerous genomes and am using the latest nightly:

    ERROR --
    ERROR stack trace

    java.lang.IllegalStateException: VC alleles [C, T*, ] not a strict subset of per read allele map alleles []
    at org.broadinstitute.gatk.utils.sam.AlignmentUtils.countBasesAtPileupPosition(AlignmentUtils.java:1408)
    at org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts.getBaseCounts(BaseCounts.java:93)
    at org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts.annotate(BaseCounts.java:78)
    at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:315)
    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:968)
    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.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 nightly-2017-04-20-g2fc0960):
    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: VC alleles [C, T*, ] not a strict subset of per read allele map alleles []
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @BWDavis
    Hi,

    Can you please submit a bug report? Instructions are here.

    Thanks,
    Sheila

  • Hi,

    has this bug been reported? I am able to reproduce this on the latest nightly build (vnightly-2017-06-15-gb466ef9).
    Do you want me to submit the sample data?

    Best,
    Rolf

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rolfschr
    Hi Rolf,

    Yes, if you can submit test data, that would be great. Instructions are here.

    Thanks,
    Sheila

  • Hi @Sheila ,

    I uploaded the sample data. The filename is gatk37-errmsg-not-a-strict-subset-of-per-read-allele-map-alleles.tar.gz
    Let me know if you cannot reproduce the error.

    Best,
    Rolf

    Issue · Github
    by Sheila

    Issue Number
    2212
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    chandrans
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rolfschr
    Hi Rolf,

    Thanks. I will take a look soon.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rolfschr
    Hi Rolf,

    Interesting, I am not sure why that has an effect. Thanks for letting us know.

    -Sheila

    P.S. I still am going to look into this. I just have not gotten to it yet.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rolfschr
    Hi Rolf,

    What reference are you using? I am not able to use the hg19 reference. It seems like you are using a version of b37 with chr added to the contigs?

    Can you upload the reference you used?

    Thanks,
    Sheila

  • Hi @Sheila,

    Sorry for that. I am using a patched hg19 with the Revised Cambridge Reference Sequence (NC_012920.1) for chrM and thus the length of chrM is different. I uploaded the data again with "correct" (plain hg19 with 16571 bases for chrM) bam file header. This should match the hg19 ref. Hope this works. The filename is

    gatk-3-7-error-message-not-a-strict-subset-of-per-read-allele-map-alleles.tar.gz

    Best,
    Rolf

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rolfschr

    Hi Rolf,

    Wonderful news! Thank you for getting back to me. I will take a look again :smiley:

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @rolfschr
    Hi again Rolf,

    Sorry for the long delay. I was able to reproduce your issue with version 3.8 too. However, the bugs in GATK3 will probably not be fixed, since we are moving to GATK4. I tried to test this in GATK4, but BaseCounts is not available yet. I will find out when/if BaseCounts will be part of GATK4 and get back to you.

    -Sheila

Sign In or Register to comment.