Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

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

Sign In or Register to comment.