Re: [svtoolkit-help] error in discovery step: invalid cnp coordinates

[Verena T. <tis...@go...>]

Hi,

sorry I just saw that someone encountered the same problem as I describe
below.

So let me please rephrase my question: Did you already find a solution to
that or did using the interim version solve the problem?

Thanks a lot
Verena

2011/12/15 Verena Tischler <tis...@go...>

> Hi,
>
> I am running GenomeSTRiP on eland mapped files and the preprocessing of
> bams works fine.
> However in the SVDiscovery step I end up with the following error
>
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0009_3706
> 91702292 91702291
>     at
> org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198)
>     at
> org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166)
>     at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599)
>     at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405)
>     at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
>     at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
>     at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
>     at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
>     at
> org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
>     at
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
>     at
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
>     at
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
>     at
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
>     at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
>     at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
>     at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
> ##### 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: Invalid cnp coordinates: DEL_P0009_3706 91702292
> 91702291
> ##### ERROR
> ------------------------------------------------------------------------------------------
>
>
> This error occurs only for one chromosome, all other chromosomes run fine
>
> Thanks a lot for your help
> Verena
>