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Old 08-02-2012, 07:19 PM   #1
eilosei
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Location: New York

Join Date: Nov 2011
Posts: 19
Question problem with MarkDuplicates in Picard

Hi,

I tried to remove duplicates by Picard but got some problem. The command I used is

PHP Code:
java -Xmx2g -Dsnappy.disable=true -jar ../picard-tools-1.70/MarkDuplicates.jar INPUT=file.sort.bam OUTPUT=file.sort.rd.bam REMOVE_DUPLICATES=true METRICS_FILE=file.rd.txt AS=true VALIDATION_STRINGENCY=LENIENT 
And the error message I got is

PHP Code:
Runtime.totalMemory()=1485766656
FAQ
:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" java.lang.OutOfMemoryErrorGC overhead limit exceeded
    at java
.util.TreeMap.put(TreeMap.java:554)
    
at java.util.TreeSet.add(TreeSet.java:238)
    
at net.sf.samtools.util.SortingCollection$MergingIterator.next(SortingCollection.java:406)
    
at net.sf.picard.sam.MarkDuplicates.generateDuplicateIndexes(MarkDuplicates.java:530)
    
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:124)
    
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:106

I used this command many times and it was the first time I got this error. Could anyone help me to understand how that happened?

Thanks!
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Old 08-03-2012, 01:13 AM   #2
shyam_la
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Location: California

Join Date: Mar 2012
Posts: 97
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It says "Out of memory". Try increasing Xmx2g to Xmx3g or Xmx4g, to assign more java heap space and try again..
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