[Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics

[Noa H. <he...@di...>]

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 he...@co... 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