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genotypeGVCF ERROR MESSAGE: 10296

ravichavravichav United StatesMember

Can someone help me fix this error? Thanks in advance

INFO 21:07:43,512 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Network is unreachable
INFO 21:07:43,513 HttpMethodDirector - Retrying request
INFO 21:07:43,516 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Network is unreachable
INFO 21:07:43,516 HttpMethodDirector - Retrying request
INFO 21:07:43,519 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Network is unreachable
INFO 21:07:43,519 HttpMethodDirector - Retrying request
INFO 21:07:43,521 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Network is unreachable
INFO 21:07:43,521 HttpMethodDirector - Retrying request
INFO 21:07:43,523 HttpMethodDirector - I/O exception (java.net.SocketException) caught when processing request: Network is unreachable
INFO 21:07:43,524 HttpMethodDirector - Retrying request

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

java.lang.ArrayIndexOutOfBoundsException: 10296
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.generatePL(ReferenceConfidenceVariantContextMerger.java:357)
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:331)
at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:134)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:200)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:119)
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:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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 http://www.broadinstitute.org/gatk
ERROR ------------------------------------------------------------------------------------------


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Guess what! I just posted a blog post on this error message :smiley:

    Can you tell us the exact command you ran? Also, can you try running ValidateVariants on your input VCF? Also, try running without -nt/-nct. Last thing, if none of those work, try the latest version of GATK.


  • ravichavravichav United StatesMember

    This is the command I used. I have a huge cohort of samples. So waht I did was combine the GVCFs hierarchically and then did a genotype GVCF, Per chromosome.

    java -Xmx24G -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R hs37d5.fa -V CASES.gvcf -V CONTROLS.gvcf -L chr_3.bed -D dbsnp_138.b37.vcf --out Ca-Co_chr3.vcf

    I am using GATK3.3 for genotypeGVCF, although I used GATK3.5 for HaplotypeCaller. All other 23 chromosomes ran well, except for this chromosome.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Did you try validating your GVCFs? Also, can you confirm the issue replicates with GenotypeGVCFs version 3.5? Why are you using two different versions for the two steps?


  • ravichavravichav United StatesMember

    The reason for using two versions is because with GATK3.5, the new variant representation (SNPs in a long spanning deletion) breaks the annotation tools like SnpEff and CAVA. I did run validateVCF and didnt find any exceptions.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    If you re-run GenotypeGVCFs on subsets of the GVCFs, do you get the same error? You'll need to try to narrow down the error to a set of files or a particular position that causes the, to generate a test case that we can debug locally.

  • ravichavravichav United StatesMember

    I got the error when I reran genotypeGVCF.

    I traced back to find the combineGVCFs script stopped after 12th chromosome, although the error log status said 100% job completed from chr 1 to chrY. I skipped the combinedGVCFs and directly ran genotypeGVCF with the single sample gvcfs directly and got the job completed for time being.

    I will rerun combineGVCFs again and look into the results again

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