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GenomeSTRiP SVPreprocess.q Java Heap Space Error

hovelsonhovelson Member
edited February 2013 in GenomeSTRiP

I'm attempting to run GenomeSTRiP's SVPreprocess.q script on a large number of samples (N=~1400; note that this is exome-sequencing data). During the MergeInsertSizeHistograms portion of the SVPreprocess.q script, the command returns prematurely and the log file reports a Java heap space error that looks like this:

INFO  12:47:02,554 HelpFormatter - Date/Time: 2013/02/07 12:47:02
INFO  12:47:02,555 HelpFormatter - ------------------------------------------------------------------
INFO  12:47:02,555 HelpFormatter - ------------------------------------------------------------------
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.TreeMap.put(TreeMap.java:571)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogram.readObject(InsertSizeHistogram.java:416)
        at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:988)
        at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1865)
        at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1770)
        at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1346)
        at java.io.ObjectInputStream.readObject(ObjectInputStream.java:368)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.readHistogram(InsertSizeHistogramFile.java:140)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.advance(InsertSizeHistogramFile.java:129)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.next(InsertSizeHistogramFile.java:107)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramFile$FileIterator.next(InsertSizeHistogramFile.java:86)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramMerger.mergeNonDisjoint(InsertSizeHistogramMerger.java:72)
        at org.broadinstitute.sv.metadata.isize.InsertSizeHistogramMerger.mergeHistograms(InsertSizeHistogramMerger.java:51)
        at org.broadinstitute.sv.apps.MergeInsertSizeHistograms.run(MergeInsertSizeHistograms.java:45)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:38)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:24)
        at org.broadinstitute.sv.apps.MergeInsertSizeHistograms.main(MergeInsertSizeHistograms.java:39)

I've experimented with -Xmx up to 16g, with the same errors every time. Given the large number of samples, is there any way to avoid running into this error? I assume similar problems might also occur with the MergeInsertSizeDistributions portion of SVPreprocess.q.

Any feedback/recommendations would be greatly appreciated - thanks very much!

Best Answer

Answers

  • hovelsonhovelson Member

    This is very helpful, Bob - thanks very much!

  • haojamhaojam Member

    Hello guys,
    I am using genomestrip (version svtoolkit_2.00.1636) for structural variations analysis but there is an error message before completing the process for sv discovery. Could you please assist me how to overcome this issue to complete the process. I hereby attached error message and command line used.

    Regards,
    Mocha

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