Re: [svtoolkit-help] Error message in SVDiscovery step

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

What version?
-Bob

On 9/1/11 11:44 AM, Kim Wong wrote:
> Hi Bob
>
> I'm running the Discovery phase using 10Mb windows and getting this error:
>
> INFO  16:04:17,165 SVDiscovery - Processing cluster
> 1:207788701-207788845 1:207889639-207889798 LR 6
> [GC 1278669K->267636K(1586432K), 1.2806820 secs]
> [GC 1375348K->267488K(1594112K), 1.2806950 secs]
> [Full GC 267488K->160084K(1605440K), 0.3875220 secs]
> #DBG: RC Cache fill    1:207778846-207888845    110000    100
> 9.229631 sec
> Error: Exception processing cluster: null
> Cluster: 1:207788701-207788845 1:207889639-207889798 LR 6
> [GC 591509K->161512K(1456512K), 1.2747640 secs]
> [Full GC 161512K->39951K(1456512K), 0.1467510 secs]
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> java.lang.IndexOutOfBoundsException
>       at java.nio.Buffer.checkIndex(Buffer.java:514)
>       at java.nio.DirectByteBuffer.get(DirectByteBuffer.java:209)
>       at
> org.broadinstitute.sv.discovery.ReadCountCache2.getReadCounts(ReadCountCache2.java:154)
>       at
> org.broadinstitute.sv.discovery.ClusterDepthModule.getReadCounts(ClusterDepthModule.java:215)
>       at
> org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:137)
>       at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:415)
>       at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:323)
>       at
> org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:173)
>       at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:165)
>       at
> org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:44)
>       at
> org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
>       at
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:85)
>       at
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:236)
>       at
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:116)
>       at
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
>       at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
>       at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
>       at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
>
>
> The parameters were set to:
>       -minimumSize 100
>       -maximumSize 1000000
>       -windowSize 10000000
>       -windowPadding 10000
>
> which gives for this window:
>
> -partitionName P0021 -filePrefix P0021 -L 1:199990000-211010000
> -searchLocus 1:200000000-209999999 -searchWindow 1:199990000-211010000
> -searchMinimumSize 100 -searchMaximumSize 1000000
>
> Any idea what is wrong?
>
> Thanks
>
> Kim
>
>
>
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