picard reOrder problem

seq_GA

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Join Date: Feb 2009

Posts: 124
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#1

picard reOrder problem

11-02-2011, 06:30 PM

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.
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seq_GA

Senior Member

Join Date: Feb 2009

Posts: 124
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#2

11-07-2011, 05:59 PM

Hi,
Any one has a solution? Thanks.
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christophpale

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Join Date: May 2010

Posts: 16
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#3

11-21-2011, 01:34 PM

Originally posted by seq_GA View Post

Hi,
Any one has a solution? Thanks.

Try
java -Xmx4g
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