Question: Memory problem with RNA-SeQC jar (v1.1.8)
gravatar for Dejian
6.3 years ago by
United States
Dejian1.3k wrote:

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>(
        at net.sf.samtools.util.StringUtil.bytesToString(
        at net.sf.samtools.BAMRecord.decodeReadName(
        at net.sf.samtools.BAMRecord.getReadName(
        at org.broadinstitute.cga.picardbased.DownsampleSam.doWork(
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
        at org.broadinstitute.cga.picardbased.CountAlignedExperimental.countBAM(
        at org.broadinstitute.cga.rnaseq.ReadCountMetrics.alignAndCountrRNA(
        at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(
        at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(

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


rna-seq • 2.3k views
ADD COMMENTlink modified 6.3 years ago by Istvan Albert ♦♦ 85k • written 6.3 years ago by Dejian1.3k
gravatar for Istvan Albert
6.3 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

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

ADD COMMENTlink written 6.3 years ago by Istvan Albert ♦♦ 85k
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