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eilosei 08-02-2012 07:19 PM

problem with MarkDuplicates in Picard

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:

Exception in thread "main" java.lang.OutOfMemoryErrorGC overhead limit exceeded
    at java
at java.util.TreeSet.add(
at net.sf.samtools.util.SortingCollection$
at net.sf.picard.sam.MarkDuplicates.generateDuplicateIndexes(
at net.sf.picard.sam.MarkDuplicates.doWork(
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
at net.sf.picard.sam.MarkDuplicates.main(

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?


shyam_la 08-03-2012 01:13 AM

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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