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  • Error while running GATK UnifiedGenotyper

    Hi everyone!
    I've been analyzing some illumina whole exome sequencing data these days. yesterday I used GATK(version 2.0) UnifiedGenotyper to call snps and indels with the following commands:
    run_gatk.sh
    -T UnifiedGenotyper
    -R GRCh37/human_g1k_v37.fasta
    -I GATK_recal_result.bam
    -glm BOTH
    --dbsnp reference/dbsnp_134.b37.vcf
    -stand_call_conf 50
    -stand_emit_conf 10
    -o raw2.vcf
    -dcov 200
    --num_threads 10

    After running theses commands, I got a vcf file which is very small(when I checked the vcf file, I found these called snps and indels are all from Chromosome1)
    The error message is as follows:
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:269)
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
    Caused by: org.broad.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files), for input source: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp
    at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:104)
    at org.broad.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:58)
    at org.broad.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:69)
    at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:182)
    at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:52)
    at org.broadinstitute.sting.gatk.executive.OutputMergeTask.merge(OutputMergeTask.java:48)
    at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:263)
    ... 6 more
    Caused by: java.io.FileNotFoundException: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:120)
    at org.broad.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:56)
    at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:96)
    ... 12 more
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.0-39-gd091f72):
    ##### 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: Unable to merge temporary Tribble output file.
    ##### ERROR ------------------------------------------------------------------------------------------
    Would you please help me solve it ? Thanks a lot
    Dona

  • #2
    You'll likely have more luck getting an answer to your question by reading the GATK documentation and then posting a question at the official GATK forums (http://gatkforums.broadinstitute.org/), as stated in your error message.

    Comment


    • #3
      As already said, ask the GATK developers, they're very responsive to questions.

      Having said that I had a very similar issue with an older release:

      /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)

      Might suggest that you've hit the per-user ulimit, on our servers I had to up the ulimit for users running UG (although the bug that was creating this issue in the 1.x series was subsequently fixed).

      Comment


      • #4
        Thanks a lot!
        I sent this error message to the server programmer, after he changed some of the system configure (in /etc/security/limit.conf), I run these commands again with num_threads reducing to 2, and it worked~

        Comment


        • #5
          thanks!
          I have solved this problem with the server programmer's help
          some of the system configre(in /etc/sequrity/limit.conf)should be changed

          Comment

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