Re: [svtoolkit-help] SVDiscovery: Code exception error

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

I will try to make the error message clearer, but the underlying problem 
looks like there is no data on fragment size distributions in
your metadata directory

/v4scratch/mmc256/ChargeS/GenomeStrip/chr1/record/metadata

I.e. no isd.hist.bin or isd.dist.bin file.
Did preprocessing complete successfully?  Or did you use a different 
metadata directory during preprocessing?

-Bob

On 7/26/12 4:59 PM, Margarida Cardoso Moreira wrote:
> Dear Bob Handsaker,
>
> First of all, I would like to thank you and your colleagues for making Genome Strip available to everyone and for helping the community using your program.
>
> I hope you can help me understand the following error that I am getting while running SVDiscovery (I am using version 1.04.939):
>
> ERROR 15:53:47,940 FunctionEdge - Error: java -Xmx4g -Djava.io.tmpdir=/tmp/1308242.scheduler.v4linux -cp /v4scratch/mmc256/svtoolkit_1.04.939//lib/SVToolkit.jar:/v4scratch/mmc256/svtoolkit_1.04.939//lib/gatk/GenomeAnalysisTK.jar:/v4scratch/mmc256/svtoolkit_1.04.939//lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /v4scratch/mmc256/human_g1k_v37.fasta -I /v4scratch/mmc256/ChargeS/GenomeStrip/chr22/ListBams.list -O /v4scratch/mmc256/ChargeS/GenomeStrip/chr1/record/P0001.discovery.vcf -md /v4scratch/mmc256/ChargeS/GenomeStrip/chr1/record/metadata -disableGATKTraversal -configFile /v4scratch/mmc256/ChargeS/GenomeStrip/chr22/genstrip_parameters_Chr22.txt -runDirectory /v4scratch/mmc256/ChargeS/GenomeStrip/chr1/record -genderMapFile /v4scratch/mmc256/ChargeS/GenomeStrip/chr22/gender_file_Chr22.txt -genomeMaskFile /v4scratch/mmc256/human_g1k_v37.mask.100.fasta -partitionName P0001 -filePrefix P0001 -L 22:1-11010000 -searchLocus 22:1-9999999 -s
>   earchWindow 22:1-11010000 -searchMinimumSize 50 -searchMaximumSize 1000000
> org.broadinstitute.sting.queue.util.JobExitException: Failed to run job.
>
> ##### ERROR ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> java.lang.NullPointerException
> 	at org.broadinstitute.sv.metadata.isize.InsertRadiusMap.init(InsertRadiusMap.java:59)
> 	at org.broadinstitute.sv.metadata.isize.InsertRadiusMap.<init>(InsertRadiusMap.java:42)
> 	at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.createClusteringRadiusMap(DeletionDiscoveryAlgorithm.java:1037)
> 	at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.initClusterModules(DeletionDiscoveryAlgorithm.java:1005)
> 	at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:317)
> 	at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:191)
> 	at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:168)
> 	at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45)
> 	at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
> 	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76)
> 	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
> 	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
> 	at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105)
> 	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
> 	at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67)
> 	at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
> ##### ERROR ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165):
> ##### ERROR
> ##### ERROR Please visit the 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: Code exception (see stack trace for error itself)
> ##### ERROR ------------------------------------------------------------------------------------------
>
> 	at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24)
> 	at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54)
> 	at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56)
> 	at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383)
> 	at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123)
> 	at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111)
> 	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
> 	at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57)
> 	at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
>
> Let me know if you need more of the output to understand the error.
>
> Thank you for your help!
>
> Margarida Cardoso Moreira
>
>
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