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

[Bob H. <han...@br...>]

Hi, Saumya,
Just going from the error message, I might guess that you specified a 
locus on the command line (e.g. using -L)
but the chromosome name does not match any name in your reference sequence.
If this isn't it, I think more detail from you will be needed.
-Bob

On 5/3/12 7:10 AM, Saumya Kumar wrote:
>
> 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
>
>
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