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Old 12-18-2011, 07:25 AM   #1
rakesh.ponnala
Junior Member
 
Location: Indianapolis, IN

Join Date: Oct 2011
Posts: 2
Default picard tools:

Hello

I have been using Picard-tools a lot recently, For one of my data-sets, I get the below error. Can you help me figure, How to resolve the issue?

Command line:

java -jar SortSam.jar I= /home/u548717/Kosena_MP_3kb/s_G1_L001_R2_001_002.sort.bam.bam O= /home/u548717/Kosena_MP_3kb/s_G1_L001_R2_001_002.noduplicates.bam SO= coordinate VALIDATION_STRINGENCY=LENIENT

Error is below:


[Sat Dec 17 09:27:15 EST 2011] net.sf.picard.sam.SortSam done. Elapsed time: 0.60 minutes.
Runtime.totalMemory()=996544512
Exception in thread "main" java.lang.OutOfMemoryError: PermGen space
at java.lang.String.intern(Native Method)
at net.sf.samtools.SAMSequenceRecord.<init>(SAMSequenceRecord.java:83)
at net.sf.samtools.SAMTextHeaderCodec.parseSQLine(SAMTextHeaderCodec.java:205)
at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:96)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:391)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:99)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:511)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:144)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:114)
at net.sf.picard.sam.SortSam.doWork(SortSam.java:61)
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.SortSam.main(SortSam.java:79)

Thanks much for the help in advance

Best,
Rakesh
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Old 12-18-2011, 08:53 AM   #2
kga1978
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Location: Boston, MA

Join Date: Nov 2010
Posts: 100
Default

Looks like you are running out of memory - try to add the following:
java -Xmx2g -jar
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