Sheila

About

Username
Sheila
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Broad Institute
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Activity

  • kmtiny

    Hi, i run into a problem when running GenotypeGVCFs. my command lines as follows:
    /scratch/gkm/software/jdk1.8.0_131/bin/java -Xmx4g -jar /scratch/gkm/software/GATK/GenomeAnalysisTK.jar \
    -T GenotypeGVCFs \
    -R /newVol/gkm/Project/malus_domestica/reference/GCA_002114115.1_ASM211411v1_genomic.fna \
    -nt 12 \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/1/1_raw.g.vcf \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/10/10_raw.g.vcf \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/11/11_raw.g.vcf \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/11-133/11-133_raw.g.vcf \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/11-39/11-39_raw.g.vcf \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/12/12_raw.g.vcf \
    --variant /newVol/gkm/Project/malus_domestica/gatk/finished/qinhe/variants/13/13_raw.g.vcf \
    ....
    -o out.vcf

    Get a error :##### ERROR --

    ERROR stack trace

    java.lang.NullPointerException
    at java.util.LinkedList$ListItr.next(LinkedList.java:893)
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.coveredByDeletion(GenotypingEngine.java:426)
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateOutputAlleleSubset(GenotypingEngine.java:387)
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:251)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:326)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:304)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:135)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
    September 20
  • ahujaa

    H
    ihave a fastq file and target bed file,
    i have aligned the fastq file with the hg38reference genome and I
    need to now call variant analysis, how should I go about it ?

    August 4