Memory problem with RNA-SeQC jar (v1.1.8)

Question

[Dejian]

When I ran RNA-SeQC jar (v1.1.8), I encountered a memory problem repeatedly. For a 2.8G bam file, I allocated memory from 4G to 40G without success. The program always threw out error messages like below:

Downsampling before aligning at rate: 0.02664358976545115
INFO    2014-08-01 00:38:37     DownsampleSam   Read 10000000 reads, kept 266113
INFO    2014-08-01 00:39:44     DownsampleSam   Read 20000000 reads, kept 531846
INFO    2014-08-01 00:43:07     DownsampleSam   Read 30000000 reads, kept 798137
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.lang.String.<init>(String.java:340)
        at net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:261)
        at net.sf.samtools.BAMRecord.decodeReadName(BAMRecord.java:331)
        at net.sf.samtools.BAMRecord.getReadName(BAMRecord.java:220)
        at org.broadinstitute.cga.picardbased.DownsampleSam.doWork(DownsampleSam.java:71)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
        at org.broadinstitute.cga.picardbased.CountAlignedExperimental.countBAM(CountAlignedExperimental.java:100)
        at org.broadinstitute.cga.rnaseq.ReadCountMetrics.alignAndCountrRNA(ReadCountMetrics.java:217)
        at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:66)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:225)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:171)
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:139)

Did anyone else encounter a similar problem? And how was it solved? Many thanks!

Answer 1

[Istvan Albert]

Allocate more heap memory to your java process, see the xmx option:

http://stackoverflow.com/questions/5374455/what-does-java-option-xmx-stand-for