Thread: [svtoolkit-help] Error message in SVDiscovery step
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From: Kim W. <kw...@sa...> - 2011-09-01 15:44:22
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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
--
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.
|
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From: Bob H. <han...@br...> - 2011-09-01 15:47:56
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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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From: Kim W. <kw...@sa...> - 2011-09-01 15:53:53
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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. |
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From: Bob H. <han...@br...> - 2011-09-01 17:53:31
|
Hi, Kim, I think I found and fixed the bug. Can you try build 785 and let me know if that solves the problem? -Bob On 9/1/11 11:53 AM, Kim Wong wrote: > 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 > |
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