Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
About Picard Jin Pan Bioinformatics 8 07-15-2014 04:55 AM
Picard Tools "loaded 0 genes" ckrna Bioinformatics 3 02-08-2012 11:26 AM
Picard tools out of memory: PermGen dgscofield Bioinformatics 4 02-04-2012 11:06 PM
using snappy java in picard tools doc.ramses Bioinformatics 3 10-04-2011 07:17 AM
What exactly is AddOrReplaceReadGroups (picard tools) doing? ocs Bioinformatics 6 06-09-2011 07:51 AM

Thread Tools
Old 12-18-2011, 07:25 AM   #1
Junior Member
Location: Indianapolis, IN

Join Date: Oct 2011
Posts: 2
Default picard tools:


I have been using Picard-tools a lot recently, For one of my data-sets, I get the below error. Can you help me figure, How to resolve the issue?

Command line:

java -jar SortSam.jar I= /home/u548717/Kosena_MP_3kb/s_G1_L001_R2_001_002.sort.bam.bam O= /home/u548717/Kosena_MP_3kb/s_G1_L001_R2_001_002.noduplicates.bam SO= coordinate VALIDATION_STRINGENCY=LENIENT

Error is below:

[Sat Dec 17 09:27:15 EST 2011] net.sf.picard.sam.SortSam done. Elapsed time: 0.60 minutes.
Exception in thread "main" java.lang.OutOfMemoryError: PermGen space
at java.lang.String.intern(Native Method)
at net.sf.samtools.SAMSequenceRecord.<init>(
at net.sf.samtools.SAMTextHeaderCodec.parseSQLine(
at net.sf.samtools.SAMTextHeaderCodec.decode(
at net.sf.samtools.BAMFileReader.readHeader(
at net.sf.samtools.BAMFileReader.<init>(
at net.sf.samtools.SAMFileReader.init(
at net.sf.samtools.SAMFileReader.<init>(
at net.sf.samtools.SAMFileReader.<init>(
at net.sf.picard.sam.SortSam.doWork(
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(
at net.sf.picard.sam.SortSam.main(

Thanks much for the help in advance

rakesh.ponnala is offline   Reply With Quote
Old 12-18-2011, 08:53 AM   #2
Senior Member
Location: Boston, MA

Join Date: Nov 2010
Posts: 100

Looks like you are running out of memory - try to add the following:
java -Xmx2g -jar
kga1978 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:51 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO