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SVPreprocess error in SVToolkit version 2.00 (build 1602)

zhaouuzhaouu hzauMember

Hi,
I got this error when I running SVPreprocess. GenomeInterval is 'chr07:8802402-9472402'.

Error massage:

Processing IRIS_313-7689/IRIS_313-7689_FCD0RHKACXX_L2/null ...
Processing IRIS_313-7689/IRIS_313-7689_FCD0RGDACXX_L2/null ...
Processing IRIS_313-7689/IRIS_313-7689_FCC0HLTACXX_L2/null ...
Exception in thread "main" java.lang.RuntimeException: Histogram iterator ended prematurely
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at org.broadinstitute.sv.apps.ReduceInsertSizeHistograms.main(ReduceInsertSizeHistograms.java:46)
Caused by: java.lang.RuntimeException: Histogram iterator ended prematurely
at org.broadinstitute.sv.metadata.isize.EmpiricalInsertSizeDistribution2.init(EmpiricalInsertSizeDistribution2.java:207)
at org.broadinstitute.sv.metadata.isize.EmpiricalInsertSizeDistribution2.(EmpiricalInsertSizeDistribution2.java:49)
at org.broadinstitute.sv.metadata.isize.EmpiricalInsertSizeDistribution.create(EmpiricalInsertSizeDistribution.java:46)
at org.broadinstitute.sv.apps.ReduceInsertSizeHistograms.run(ReduceInsertSizeHistograms.java:63)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
... 5 more
INFO 08:50:26,010 QGraph - Writing incremental jobs reports...
INFO 08:50:26,939 QGraph - 7094 Pend, 0 Run, 1 Fail, 1422 Done
INFO 08:50:27,095 QCommandLine - Writing final jobs report...
INFO 08:50:27,115 QCommandLine - Done with errors
INFO 08:50:27,941 QGraph - -------
INFO 08:50:27,941 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/hzhao/tmp/svtoolkit' '-cp' '/home/hzhao/software/svtoolkit/lib/SVToolkit.jar:/home/hzhao/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/hzhao/software/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/hzhao/software/svtoolkit/lib/SVToolkit.jar:/home/hzhao/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/hzhao/software/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/home/hzhao/my_data/GATK_res/sv_test/metadata/isd.hist.bin' '-O' '/home/hzhao/my_data/GATK_res/sv_test/metadata/isd.dist.bin'
INFO 08:50:27,942 QGraph - Log: /home/hzhao/my_data/GATK_res/sv_test/logs/SVPreprocess-1423.out
INFO 08:50:27,943 QCommandLine - Script failed: 7094 Pend, 0 Run, 1 Fail, 1422 Done

I have tried to remove this bam file (IRIS_313-7689.bam), but other bam files can also occur same massage. How can I overcome this just now? And how this problem occurs? Thanks.

Answers

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