[svtoolkit-help] Having trouble with SVPreprocess
Status: Beta
Brought to you by:
bhandsaker
From: Homann, O. <oh...@am...> - 2015-02-25 17:03:08
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Hello, I'm running into difficulties trying to run SVPreprocess, and was hoping you might have some ideas about what has gone wrong. After a while the run fails with a (seemingly uninformative) ReduceInsertSizeHistograms error (see end of e-mail). Oddly, I can run that exact same command at the command line (just changing the output name), and it works without reporting any errors. In both cases an output file of the same size is created, which makes me wonder if this is even the step that is truly failing. A few other observations/comments: * I note that the log appends 'null' to the name of the sample it is processing... is this a clue to something being amiss? * I've had to build my own genome bundle because my alignments include the hs37d5 decoy "chromosome". Perhaps I did something odd there that is contributing to the problem? * I am doing this test using the Shell mode since I can't seem to get Queue to work with LSF 9 and drmaa. Any suggestions would be greatly appreciated. Regards, Oliver Homann ================================================================== Error from Shell SVPreprocess run ================================================================== ERROR 17:34:50,817 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/mypath/scripts/.queue/tmp' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/mypath/output/isd/mysample.hist.bin' '-O' '/mypath/output/isd/mysample.dist.bin' ERROR 17:34:50,830 FunctionEdge - Contents of /mypath/output/logs/SVPreprocess-6.out: INFO 16:35:09,560 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,562 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 16:35:09,566 HelpFormatter - Program Args: -I /mypath/output/isd/mysample.hist.bin -O /mypath/output/isd/mysample.dist.bin INFO 16:35:09,569 HelpFormatter - Executing as me...@my... on Linux 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 16:35:09,570 HelpFormatter - Date/Time: 2015/02/24 16:35:09 INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- Processing mysample/mysample/null ... INFO 16:35:20,573 CommandLineProgram - Program completed. ================================================================== |