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  • 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!

  • #2
    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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