Re: [svtoolkit-help] Discovery error - Invalid cnp coordinates

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

It's a bug.  What version are you using?
You could try the latest interim release at 
ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/ and see if 
it helps.
Also, if you could look in, e.g. for the first one, the 
P0011.discovery.clusters.dat file in the run directory and send me the 
tail of this file
(anything after the event DEL_P0011_116) that would be helpful.  Or the 
whole file if it is not too big.
I can't promise when I will get time to look at it, though.
-Bob

On 11/17/11 2:26 PM, Ashish Kumar wrote:
>
> Hi Bob,
>
> Following are two errors that I encounter while running the 
> SVDiscovery process.
>
> Could you please assist what is being referred as invalid cnp 
> coordinates? Is that some alignment issue?
>
> Thanks,
>
> Ashish.
>
> 1.Stack trace
>
> Error: Exception processing cluster: Invalid cnp coordinates: 
> DEL_P0011_116 107088044 107088043
>
> Cluster: 1:107087601-107087956 1:107088131-107088520 LR 2
>
> INFO  00:04:16,357 GATKRunReport - Aggregating data for run report
>
> [GC 987003K->47999K(1502336K), 0.0129670 secs]
>
> [Full GC 47999K->31291K(1502336K), 0.1004900 secs]
>
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
> ##### ERROR stack trace
>
> java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0011_116 
> 107088044 107088043
>
>                 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_P0011_116 107088044 
> 107088043
>
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
> 2.Stack trace
>
> Error: Exception processing cluster: Invalid cnp coordinates: 
> DEL_P0019_113 187483130 187483129
>
> Cluster: 1:187482695-187483064 1:187483195-187483568 LR 2
>
> INFO  01:10:09,053 GATKRunReport - Aggregating data for run report
>
> [GC 1125151K->46166K(1486208K), 0.0125410 secs]
>
> [Full GC 46166K->24635K(1486208K), 0.1061040 secs]
>
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
> ##### ERROR stack trace
>
> java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0019_113 
> 187483130 187483129
>
>                 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_P0019_113 187483130 
> 187483129
>
> ##### ERROR 
> ------------------------------------------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------------
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