[svtoolkit-help] Discovery error - Invalid cnp coordinates

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

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 ------------------------------------------------------------------------------------------