Thank you very much. Yes, I was missing this option in my command. Since I am working in WGS of Human Samples so this option is kind of necessary to use in order to handle large data sets while processing/aligning reads. Moreover, now I am running command like /usr/bin/java -Xmx40g -jar /usr/local/picard-tools-1.129/picard.jar ...., and it's working. Regards, Ravi.
AddOrReplaceReadGroups by Picard related error "Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded"
Hi, I am encountering this error while adding 'Group information using Picard'. It would be great if anybody suggest me a solution for this error.
Command:
/usr/bin/java \
-jar /usr/local/picard-tools-1.129/picard.jar \
AddOrReplaceReadGroups \
I=ETH002331.bwa.sam \
O=ETH002331.bam \
SO=coordinate \
ID=2331 \
PL=Illumina \
PU=2331 \
SM=2331 \
LB=2331 \
MAX_RECORDS_IN_RAM=10000000 \
TMP_DIR=/san/illumina_two/tmp_rsindhu/
Output/Error:
[Tue Oct 06 10:02:55 EDT 2015] picard.sam.AddOrReplaceReadGroups INPUT=ETH002331.bwa.sam OUTPUT=ETH002331.bam SORT_ORDER=coordinate RGID=2331 RGLB=2331 RGPL=Illumina RGPU=2331 RGSM=2331 TMP_DIR=[/san/illumina_two/tmp_rsindhu] MAX_RECORDS_IN_RAM=10000000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Oct 06 10:02:55 EDT 2015] Executing as rsindhu@node13 on Linux 2.6.18-164.15.1.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13; Picard version: 1.129(b508b2885562a4e932d3a3a60b8ea283b7ec78e2_1424706677) IntelDeflater
INFO 2015-10-06 10:02:55 AddOrReplaceReadGroups Created read group ID=2331 PL=Illumina LB=2331 SM=2331
INFO 2015-10-06 10:03:04 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 8s. Last read position: 3:93,470,726
INFO 2015-10-06 10:03:18 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 13s. Last read position: 11:54,692,144
INFO 2015-10-06 10:03:46 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 27s. Last read position: 1:9,626,979
INFO 2015-10-06 10:03:53 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 7s. Last read position: 15:36,735,360
INFO 2015-10-06 10:04:16 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 22s. Last read position: 12:68,352,108
INFO 2015-10-06 10:04:36 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 19s. Last read position: 1:204,840,100
INFO 2015-10-06 10:04:49 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 13s. Last read position: 1:163,618,828
INFO 2015-10-06 10:05:17 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 28s. Last read position: 6:129,383,605
INFO 2015-10-06 10:05:46 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 28s. Last read position: 4:87,904,801
INFO 2015-10-06 10:09:01 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 194s. Last read position: 7:102,840,920
INFO 2015-10-06 10:11:35 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 154s. Last read position: 13:24,434,813
INFO 2015-10-06 10:11:49 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 14s. Last read position: 7:92,219,814
INFO 2015-10-06 10:12:03 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 13s. Last read position: 3:70,583,119
INFO 2015-10-06 10:12:19 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 16s. Last read position: 3:14,135,029
INFO 2015-10-06 10:12:28 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 9s. Last read position: 5:178,739,899
INFO 2015-10-06 10:12:41 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 12s. Last read position: 8:112,973,946
INFO 2015-10-06 10:12:48 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 7s. Last read position: 1:125,179,853
INFO 2015-10-06 10:13:13 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 25s. Last read position: 2:71,028,202
INFO 2015-10-06 10:13:56 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 42s. Last read position: 9:60,641,119
[Tue Oct 06 10:29:47 EDT 2015] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 26.87 minutes.
Runtime.totalMemory()=6657409024
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at htsjdk.samtools.util.StringUtil.stringToBytes(StringUtil.java:315)
at htsjdk.samtools.SAMRecord.setReadString(SAMRecord.java:216)
at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:315)
at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:248)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:236)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:212)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:527)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:501)
at picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:116)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
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I am not sure about default memory picard uses. See if you can allocate more memory to JVM by using -Xmx option. Example command looks more like this: java -jar picard.jar -Xmx 4G <rest of arguments>. Please do search online on how to use -Xmx.
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seems like you are running out of memory here.
Yes, that's written in the output message. Is addition of extra memory is the only alternative ?.