VariantsToBinaryPed Throwing IndexOutofBoundsException

tottlefieldstottlefields Newmarket, UKMember
edited April 2017 in Ask the GATK team

Hi All,

I am trying to use the GATK v3.7 VariantsToBinaryPed on my multi-sample VCF file to create PLINK files. However it is throwing an error, the stack trace is shown below...

##### ERROR --
##### ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -1
        at htsjdk.variant.variantcontext.GenotypeLikelihoods.getGQLog10FromLikelihoods(GenotypeLikelihoods.java:220)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.checkGQIsGood(VariantsToBinaryPed.java:442)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getStandardEncoding(VariantsToBinaryPed.java:406)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.getEncoding(VariantsToBinaryPed.java:398)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.writeIndividualMajor(VariantsToBinaryPed.java:282)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:267)
        at org.broadinstitute.gatk.tools.walkers.variantutils.VariantsToBinaryPed.map(VariantsToBinaryPed.java:103)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
        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.TraverseLociNano.traverse(TraverseLociNano.java:144)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
        at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        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)
##### ERROR ------------------------------------------------------------------------------------------
##### 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: -1
##### ERROR ------------------------------------------------------------------------------------------

My command...

java -Xmx32g -Djava.io.tmpdir=$HOME/javatempdir -jar /opt/gatk3.7/GenomeAnalysisTK.jar \
        -T VariantsToBinaryPed \
        -R /geneticsdata/alces-flight-image/canfam3/ensembl/canfam3.fasta \
        -V /geneticsdata/wgs_ens/ens_WGS_87_VEP.vcf.gz \
        --minGenotypeQuality 10 \
        -m /geneticsdata/wgs_ens/ens_WGS_87_metadata.fam \
        -bed /geneticsdata/wgs_ens/ens_WGS_87.bed \
        -bim /geneticsdata/wgs_ens/ens_WGS_87.bim \
        -fam /geneticsdata/wgs_ens/ens_WGS_87.fam

The line of the VCF file where the script is falling over...

1       668     .       C       T       153.78  .       AC=7;AF=0.233;AN=30;BaseQRankSum=-7.270e-01;ClippingRankSum=0.727;DP=48;ExcessHet=0.0117;FS=0.000;InbreedingCoeff=0.3446;MLEAC=7;MLEAF=0.233;MQ=33.46;MQ0=0;MQRankSum=0.727;QD=25.63;ReadPosRankSum=0.727;SOR=0.368;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||||||SNV||||||||||||||||||||||||||||||||||      GT:AD:DP:GQ:PGT:PID:PL  0/0:1,0:1:3:.:.:0,3,31  0/0:1,0:1:3:.:.:0,3,32  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,57  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,65  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:16,0:16:45:.:.:0,45,675     ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   1/1:0,3:3:9:.:.:92,9,0  1/1:0,1:1:3:.:.:10,3,0  1/1:0,3:3:9:.:.:102,9,0 0/1:3,1:4:8:0|1:668_C_T:8,0,58  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,21  ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,12  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:8,0:8:18:.:.:0,18,270       ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:1,0:1:3:.:.:0,3,30  0/0:1,0:1:3:.:.:0,3,34  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:1,0:1:.:.:.:0,0,0      0/0:1,0:1:3:.:.:0,3,32  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0      ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0

I'm probably doing something totally stupid (apologies if I am), but please can somebody help me out?

Thanks,
Ellen.

Answers

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