Hi :
I am trying to use your tool SamtoFastq on a very large full genome BAM
file ( 127GB ) to extract R1 and R2. But every time i try to run the
tool it gives me this error: (after a long time)
INFO 2014-12-04 05:53:44 SamToFastq Processed 1,332,000,000
records. Elapsed time: 04:29:26s. Time for last 1,000,000: 132s.
Last read position: hs37d5:21,480,730
INFO 2014-12-04 05:57:06 SamToFastq Processed 1,333,000,000
records. Elapsed time: 04:32:48s. Time for last 1,000,000: 202s.
Last read position: hs37d5:21,715,030
INFO 2014-12-04 06:01:47 SamToFastq Processed 1,334,000,000
records. Elapsed time: 04:37:29s. Time for last 1,000,000: 280s.
Last read position: hs37d5:22,206,196
[Thu Dec 04 06:08:35 CET 2014] picard.sam.SamToFastq done. Elapsed time:
284.29 minutes.
Runtime.totalMemory()=8485076992
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.BAMRecord.decodeBaseQualities(BAMRecord.java:317)
at htsjdk.samtools.BAMRecord.getBaseQualities(BAMRecord.java:279)
at htsjdk.samtools.SAMRecord.isValid(SAMRecord.java:1636)
at
htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:642)
at
htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:628)
at
htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:598)
at
htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:514)
at
htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:488)
at picard.sam.SamToFastq.doWork(SamToFastq.java:149)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
at picard.sam.SamToFastq.main(SamToFastq.java:137)
In the beginning of my project i had some files of 80-100 GB which
already gave me problems with the GCoverhead limit. There for i changed
the setting of GCoverhead to 0.98 instead of your default which was +-
0.50.
This helped for the somewhat smaller files. Can you please give me an
indication on how to fix this? I read on some previous post:
*Re: [Samtools-help] Out of memory samtofastq
<http://sourceforge.net/p/samtools/mailman/message/27904292/>*
From: Joachim Jacob <joachim.jacob@vi...> - 2011-08-04 08:28:35
*Attachments:*Message as HTML
<http://sourceforge.net/p/samtools/mailman/attachment/4E3A582B.1010809%40vib.be/1/>
Hi all,
I have apparently fixed the issue by using these parameters (24 CPU
machine, with 96GB RAM):
*java -Xmx40g -jar -XX:-UseGCOverheadLimit -XX:-UseParallelGC *
Steadily but firmly the fastq file is being filled.
Joachim
This still doesnt work for my big BAM file. I am currently retrying it
with more cores and higher memory. Keep you updated if that works.
Best,
Sander
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