runtime error in CoveredByNSamplesSites

Dear team,

I would like to inform you that I encountered a runtime error in CoveredByNSamplesSites for which I did not find a discussion the forum.
Eva

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

java.lang.RuntimeException: there are more then one vc: 2
at org.broadinstitute.sting.gatk.walkers.diagnostics.CoveredByNSamplesSites.map(CoveredByNSamplesSites.java:99)
at org.broadinstitute.sting.gatk.walkers.diagnostics.CoveredByNSamplesSites.map(CoveredByNSamplesSites.java:75)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:268)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:256)
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.TraverseLociNano.traverse(TraverseLociNano.java:145)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
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 2.4-9-g532efad):
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: there are more then one vc: 2
ERROR ------------------------------------------------------------------------------------------

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Eva,

    Can you please post your command line, and tell me if you have validated your input files?

  • evakoeevakoe Member

    Sure, my command line was:

    java -Xmx2g -jar GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T CoveredByNSamplesSites -V variants.vcf -out intervals -minCov 5 -percentage 0.8

    I just ran the ValidateVariants program on my vcf file and (with -type ALL -warnOnErrors), I get many of these warnings:

    WARN 17:18:21,509 ValidateVariants - ***** the Allele Count (AC) tag is incorrect for the record at position 1:2241376, 6 vs. 6 *****
    WARN 17:18:23,125 ValidateVariants - ***** the Allele Count (AC) tag is incorrect for the record at position 1:7828173, 5 vs. 5 *****
    WARN 17:18:23,163 ValidateVariants - ***** the Allele Count (AC) tag is incorrect for the record at position 1:7980708, 4 vs. 4 *****
    WARN 17:18:23,354 ValidateVariants - ***** the Allele Count (AC) tag is incorrect for the record at position 1:8877520, 8 vs. 8 *****

    I am a bit surprised, because I only used GATK tools for my processing (besides BWA and Picard MD) and used your recommondations.

    ValidateVariants with -type NONE gives:

    Successfully validated the input file. Checked 94595 records with no failures.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Did you do your earlier processing with an older version of GATK? In the past the AC tag was not getting processed properly when VCFs were merged or split.

    But I don't think that's responsible for the runtime error you encountered. Can you please try running your command again using the latest nightly build? (see Downloads page) This is to check whether the error still occurs with our latest development version.

  • evakoeevakoe Member

    CoveredByNSamplesSites ran successfully with the latest nightly build on the same input.

    And yes, my vcf file was created with GATK 2.4-7 and when I encountered the error in CoveredByNSamplesSites, I downloaded 2.4-9 and also used this version to run ValidateVariants.

    Well I guess the matter is resolved then.
    Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Glad to hear it! FYI the next official release (2.5), which contains all these fixes, is coming pretty soon.

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