problem with MarkDuplicates in Picard

[eilosei]

Hi,

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

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

Runtime.totalMemory()=1485766656
FAQ:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" java.lang.OutOfMemoryError: GC 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!

[shyam_la]

It says "Out of memory". Try increasing Xmx2g to Xmx3g or Xmx4g, to assign more java heap space and try again..