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  • Help!Error: the contig index is greater then the stored sequence count

    Hi all

    I have encountered the same problem as this http://seqanswers.com/forums/showthread.php?t=6937

    Fowllowing the instruction on Local realignment around indels, I was able to go though the first step. However, the second step has some errors.
    In additon, my GATK is the latest one. And, I dealed with mitochondrial genome, size of which is rather small for only 20+M.

    Can anybody give some advice?

    Here is the log:
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    org.broadinstitute.sting.utils.exceptions.Reviewed StingException: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
    at org.broadinstitute.sting.utils.GenomeLocParser.exc eptionOnInvalidGenomeLoc(GenomeLocParser.java:443)
    at org.broadinstitute.sting.utils.GenomeLocParser.cre ateGenomeLoc(GenomeLocParser.java:403)
    at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.isOutOfOrder(VerifyingSamIterator.java: 51)
    at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.verifyRecord(VerifyingSamIterator.java: 41)
    at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.next(VerifyingSamIterator.java:34)
    at org.broadinstitute.sting.gatk.iterators.VerifyingS amIterator.next(VerifyingSamIterator.java:18)
    at org.broadinstitute.sting.gatk.filters.CountingFilt eringIterator.getNextRecord(CountingFilteringItera tor.java:106)
    at org.broadinstitute.sting.gatk.filters.CountingFilt eringIterator.next(CountingFilteringIterator.java: 82)
    at org.broadinstitute.sting.gatk.filters.CountingFilt eringIterator.next(CountingFilteringIterator.java: 42)
    at org.broadinstitute.sting.gatk.iterators.PrivateStr ingSAMCloseableIterator.next(StingSAMIteratorAdapt er.java:100)
    at org.broadinstitute.sting.gatk.iterators.PrivateStr ingSAMCloseableIterator.next(StingSAMIteratorAdapt er.java:84)
    at org.broadinstitute.sting.gatk.datasources.simpleDa taSources.SAMDataSource.fillShard(SAMDataSource.ja va:375)
    at org.broadinstitute.sting.gatk.datasources.shards.R eadShardStrategy.advance(ReadShardStrategy.java:15 4)
    at org.broadinstitute.sting.gatk.datasources.shards.R eadShardStrategy.<init>(ReadShardStrategy.java:100 )
    at org.broadinstitute.sting.gatk.datasources.shards.S hardStrategyFactory.shatter(ShardStrategyFactory.j ava:73)
    at org.broadinstitute.sting.gatk.datasources.shards.S hardStrategyFactory.shatter(ShardStrategyFactory.j ava:55)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine .getShardStrategy(GenomeAnalysisEngine.java:333)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine .execute(GenomeAnalysisEngine.java:100)
    at org.broadinstitute.sting.gatk.CommandLineExecutabl e.execute(CommandLineExecutable.java:97)
    at org.broadinstitute.sting.commandline.CommandLinePr ogram.start(CommandLineProgram.java:244)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main (CommandLineGATK.java:87)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.4705):
    ##### ERROR
    ##### ERROR Please visit to 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
    ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
    ##### ERROR
    ##### ERROR MESSAGE: Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count
    ##### ERROR ------------------------------------------------------------------------------------------

  • #2
    Hi, the problem was solved by just download the offical reference sequences.
    Thanks all.

    Comment


    • #3
      Originally posted by HongxiangZheng View Post
      Hi, the problem was solved by just download the offical reference sequences.
      Thanks all.
      I have download the offical reference sequences.
      but the erro still appear in chrX and chrY.~~

      Comment


      • #4
        My problem also was solved .You must be use the same reference in the aligned and GATK
        ~~

        Comment

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