Question: AddOrReplaceReadGroups by Picard related error "Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded"
0
gravatar for ravi.uhdnis
3.9 years ago by
ravi.uhdnis170
United States
ravi.uhdnis170 wrote:

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)

sequencing alignment assembly • 5.7k views
ADD COMMENTlink modified 3.9 years ago by cpad011211k • written 3.9 years ago by ravi.uhdnis170

seems like you are running out of memory here.

ADD REPLYlink written 3.9 years ago by Adrian Pelin2.3k

Yes, that's written in the output message. Is addition of extra memory is the only alternative ?.

ADD REPLYlink written 3.9 years ago by ravi.uhdnis170
1
gravatar for cpad0112
3.9 years ago by
cpad011211k
India
cpad011211k wrote:

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 arguement>. Please do search online on how to use -Xmx.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by cpad011211k

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.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by ravi.uhdnis170
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