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

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

SVToolkit version 1.04 (build 683). (This isn't one of your main 
releases but this version allows me to format the lsf memory 
requirements a little differently for our system)


Kim



On 01/09/11 16:47, Bob Handsaker wrote:
> 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
>>
>>
>>
>>
>>
>>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.