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]>
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] 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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>
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>
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