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ERROR stack trace

MoneteMonete BrazilMember

Hi,

I ran genotypeGVCF (version 3.8) with an input from 91 WES samples combined (with combinegvcf). I got an error and I couldn't find a solution here.

My command line include the options: --dbsnp, --annotateNDA, --sample_ploidy 182, --useNewAFCalculator

The error log which I had:

ERROR --
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 20
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods.getNumLikelihoodElements(GeneralPloidyGenotypeLikelihoods.java:440)
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods.subsetToAlleles(GeneralPloidyGenotypeLikelihoods.java:339)
at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.IndependentAllelesExactAFCalculator.subsetAlleles(IndependentAllelesExactAFCalculator.java:494)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:292)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:327)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:305)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:136)
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: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 SITE GATK
ERROR
ERROR MESSAGE: 20
ERROR ------------------------------------------------------------------------------------------

Does anyone could help me?

Sorry for any inconvenience or if I asked in wrong place.

Thank you for your time and patience

Best Answers

Answers

  • MoneteMonete BrazilMember
    edited October 2018

    Hi @bhanuGandham

    My command (with ERROR described above) was:

    java -Xmx480000m -jar $gatkPath -R hg19.fasta -T GenotypeGVCFs -nt 20 \
    --dbsnp dbsnp_138.hg19.vcf --variant ${fileName}-cohort_COMBINED.g.vcf.gz \
    --annotateNDA --sample_ploidy 182 --useNewAFCalculator \
    --out ${fileName}-cohort_GENOTYPEGVCF_v2.vcf.gz;
    

    The ploidy option is 182 because I have 91 samples (91 x 2 = 182) combined.

    But, I've made a test with a basic command (below and without options) and everything ran ok.

    java -Xmx480000m -jar $gatkPath \
    -R hg19.fasta -T GenotypeGVCFs -nt 20 --dbsnp dbsnp_138.hg19.vcf \
    --variant ${fileName}-cohort_COMBINED.g.vcf.gz \
    --out ${fileName}-cohort_GENOTYPEGVCF.vcf.gz;
    

    Thank you.

    Best,

    Monete

    Post edited by Monete on
  • MoneteMonete BrazilMember
    edited October 2018

    Hi @bhanuGandham

    Thanks for your reply.

    For now, we will continue on 3.8 version in order to try to replicate some results. Also, I believe it's important to say this error didn't happen with commands below (despite the same input datasets).

    java -Xmx40g -jar $gatkPath \
    -R hg19.fasta -T GenotypeGVCFs -nt 20 --dbsnp dbsnp_138.hg19.vcf \
    --variant ${fileName}-cohort_COMBINED.g.vcf.gz \
    --out ${fileName}-cohort_GENOTYPEGVCF.vcf.gz;
    

    and

    java -Xmx480000m -jar $gatkPath -R hg19.fasta -T GenotypeGVCFs -nt 20 \
    --dbsnp dbsnp_138.hg19.vcf --variant ${fileName}-cohort_COMBINED.g.vcf.gz \
    --annotateNDA --useNewAFCalculator \
    --out ${fileName}-cohort_GENOTYPEGVCF.vcf.gz;
    

    and

    java -Xmx480000m -jar $gatkPath -R hg19.fasta -T GenotypeGVCFs -nt 20 \
    --dbsnp dbsnp_138.hg19.vcf --variant ${fileName}-cohort_COMBINED.g.vcf.gz \
    --annotateNDA --sample_ploidy 182 \
    --out ${fileName}-cohort_GENOTYPEGVCF.vcf.gz;
    

    Soon, we intend to upgrade to gatk4 and if I notice this error I'll get back here.

    Thanks again.

    Best,

    Monete

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Sounds good @Monete, thanks for the update

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