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  • picard reOrder problem

    Hi,
    I am getting the following error while trying to use picard ReorderSam. The bam file is around 29G size.

    Code:
     java -Xmx30G -jar /picard-tools-1.55/ReorderSam.jar I=test.bam O=test_reOrder.bam R=hg19.fa
    [Wed Nov 02 16:30:11 SGT 2011] net.sf.picard.sam.ReorderSam done. Elapsed time: 50.22 minutes.
    Runtime.totalMemory()=11533090816
    Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /tmp/userrig/sortingcollection.7495261805918270421.tmp (Too many open files)
    at net.sf.samtools.util.SortingCollection$FileRecordIterator.<init>(SortingCollection.java:445)
    at net.sf.samtools.util.SortingCollection$MergingIterator.<init>(SortingCollection.java:384)
    at net.sf.samtools.util.SortingCollection.iterator(SortingCollection.java:254)
    at net.sf.samtools.util.SortingCollection.iterator(SortingCollection.java:43)
    at net.sf.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:177)
    at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:120)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
    at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
    Caused by: java.io.FileNotFoundException: /tmp/userrig/sortingcollection.7495261805918270421.tmp (Too many open files)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:120)
    at net.sf.samtools.util.SortingCollection$FileRecordIterator.<init>(SortingCollection.java:439)
    ... 8 more
    Please let me know a way to overcome this problem. Thanks.

  • #2
    Hi,
    Any one has a solution? Thanks.

    Comment


    • #3
      Originally posted by seq_GA View Post
      Hi,
      Any one has a solution? Thanks.
      Try
      java -Xmx4g

      Comment

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