Hi,
I tried to remove duplicates by Picard but got some problem. The command I used is
And the error message I got is
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!
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
PHP Code:
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!
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