Hello,
I am trying to SortSam a 5 gb sam file using:
/usr/bin/java -jar /home/ubuntu/software_stack//picard/dist/picard.jar
SortSam INPUT=/home/ubuntu/output//SRR1219520//out_aligned.sam
OUTPUT=/home/ubuntu/output//SRR1219520//out_SO.bam SORT_ORDER=coordinate
VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
I run into error and get this message:
[Mon Dec 22 05:55:27 UTC 2014] picard.sam.SortSam
INPUT=/home/ubuntu/output/SRR1219520/out_aligned.sam
OUTPUT=/home/ubuntu/output/SRR1219520/out_SO.bam SORT_ORDER=coordinate
VALIDATION_STRINGENCY=LENIENT MAX_RECORDS_IN_RAM=500 CREATE_INDEX=true
VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false
[Mon Dec 22 05:55:27 UTC 2014] Executing as ubuntu@localhost on Linux
3.13.0-36-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32; Picard
version: 1.126() JdkDeflater
[Mon Dec 22 05:55:58 UTC 2014] picard.sam.SortSam done. Elapsed time: 0.50
minutes.
Runtime.totalMemory()=7223115776
To get help, see
http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Requested array size
exceeds VM limit
at java.util.Arrays.copyOf(Arrays.java:2367)
at
java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
at
java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
at java.lang.StringBuilder.append(StringBuilder.java:132)
at
htsjdk.samtools.SAMTextHeaderCodec.advanceLine(SAMTextHeaderCodec.java:131)
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:86)
at htsjdk.samtools.SAMTextReader.readHeader(SAMTextReader.java:195)
at htsjdk.samtools.SAMTextReader.<init>(SAMTextReader.java:62)
at htsjdk.samtools.SAMTextReader.<init>(SAMTextReader.java:71)
at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:703)
at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:178)
at htsjdk.samtools.SAMFileReader.<init>(SAMFileReader.java:148)
at picard.sam.SortSam.doWork(SortSam.java:71)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
Following one of the FAQ's i tried reducing MAX_RECORDS_IN_RAM (to as low
as 500) and still get same error. I tried ValidateSamFile and again same
error. I checked sam file for abnormality but it looks fine (normal 101bp
reads).
I'm using a 64 bit ubuntu AWS-EC2 instance with 30Gb ram and java version
"1.7.0_65" (OpenJDK Runtime Environment (IcedTea 2.5.3)
(7u71-2.5.3-0ubuntu0.14.04.1), OpenJDK 64-Bit Server VM (build 24.65-b04,
mixed mode)).
Kindly help.
--
Regards
Neeraj Suthar
Data Scientist
InterpretOmics India Pvt. Ltd.
#329, 7th Main, HAL II Stage,
Indira Nagar, 80 Feet Road,
Bangalore – 560008
India
Cell: +917760268157
URL: www.interpretomics.co
*Statement of Confidentiality:* This email message and any attachments are
intended for the sole use of the addressee(s) and may contain confidential
and/or privileged information. If you are not an intended recipient,
please contact me via email reply and destroy all copies of this message
and any attachments.
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
