Hi Nils, I actually tried that and it worked, didn’t have the chance to post
this update before.
Thank you,
Noa
From: Nils Homer
Date: Monday, June 22, 2015 at 9:22 AM
To: henig
Cc:
"[email protected]<mailto:[email protected]>"
Subject: Re: [Samtools-help] "OutOfMemoryError: Java heap space" exception in
Picard CollectMultipleMetrics
Hey Noa,
could you try with more memory (say 8g?) and if that doesn't work post back
here? In the latter case we would likely need your input data to reproduce,
N
On Sun, Jun 21, 2015 at 11:06 AM, Noa Henig
<[email protected]<mailto:[email protected]>> wrote:
Hi,
I’m running picard to get some metrics and CollectMultipleMetrics crashed with
the following exception:
[Sun Jun 21 00:27:08 EDT 2015] picard.analysis.CollectMultipleMetrics
INPUT=/sge_tmp/KP1.bam OUTPUT=/mnt/home/Noa/Analysis/KP1
PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics,
QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle,
CollectGcBiasMetrics, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics]
REFERENCE_SEQUENCE=/mnt/home/ref/hs38DH/hs38DH.fa ASSUME_SORTED=true
STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Sun Jun 21 00:27:08 EDT 2015] Executing as
[email protected]<mailto:[email protected]> on Linux
2.6.32-279.14.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM
1.8.0_40-b26; Picard version:
1.133(e59e06df06b813896b14ce055d5fb8563d06cabf_1433947038) IntelDeflater
[Sun Jun 21 00:38:48 EDT 2015] picard.analysis.CollectMultipleMetrics done.
Elapsed time: 11.66 minutes.
Runtime.totalMemory()=1740636160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at
picard.analysis.CollectGcBiasMetrics.calculateAllGcs(CollectGcBiasMetrics.java:188)
at
picard.analysis.CollectGcBiasMetrics.setup(CollectGcBiasMetrics.java:137)
at
picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:98)
at
picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:199)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at
picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
I tried to run with –Xmx2g or –Xmx4g but there was no difference, and also ran
ValidateSamFile as recommended in the FAQ but did not receive errors.
The java version is 1.8.0_40.
The bam files are smaller than 1g and the same setup has been running fine for
many other bam files, any suggestions what could be the problem
Thanks,
Noa
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