svtoolkit-help

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

[Verena T. <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

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
>

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

[Ashish K. <as...@we...>]

Hi,
The interim release that Bob pointed me to, solved the problem for me.

Best,
Ashish.



From: Verena Tischler [mailto:tis...@go...]
Sent: 15 December 2011 15:23
To: svt...@li...
Subject: Re: [svtoolkit-help] error in discovery step: invalid cnp coordinates

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...<mailto: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

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

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

If it still happens in the latest interim release, let me know.
-Bob

On 12/15/11 9:23 AM, Verena Tischler wrote:
> 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... 
> <mailto: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
>
>
>
>
> ------------------------------------------------------------------------------
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