[svtoolkit-help] Error message in SVDiscovery step

[Kim W. <kw...@sa...>]

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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