[svtoolkit-help] ERROR MESSAGE: Parameters to GenomeLocParser are incorrect: the contig index is less than 0

[Saumya K. <s....@ha...>]

Hello,

I am using Genome Strip on one of the bam files and it generates this error:

ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Parameters to GenomeLocParser are incorrect: the contig index is less than 0
        at org.broadinstitute.sting.utils.GenomeLocParser.exceptionOnInvalidGenomeLoc(GenomeLocParser.java:427)
        at org.broadinstitute.sting.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:390)
        at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.isOutOfOrder(VerifyingSamIterator.java:47)
        at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.verifyRecord(VerifyingSamIterator.java:36)
        at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:29)
        at org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator.next(VerifyingSamIterator.java:13)
        at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:106)
        at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:82)
        at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.next(CountingFilteringIterator.java:42)
        at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:100)
        at org.broadinstitute.sting.gatk.iterators.PrivateStringSAMCloseableIterator.next(StingSAMIteratorAdapter.java:84)
        at org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource.fillShard(SAMDataSource.java:436)
        at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.advance(ReadShardStrategy.java:179)
        at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.next(ReadShardStrategy.java:129)
        at org.broadinstitute.sting.gatk.datasources.shards.ReadShardStrategy.next(ReadShardStrategy.java:44)
        at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:172)
        at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:144)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:52)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

I have adapted discovery.sh script according to my bam files, but it is giving this sort of error. I couldn't find anything similar in the archive list, could anyone please suggest what might be the problem?

Thanks,
Saumya



This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm