To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

FilterSamReads: java.lang.OutOfMemoryError: Java heap space

How to estimate the memory use (-Xmx?G) when using FilterSamReads? I always get the errors:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.regex.Pattern$Start.(Pattern.java:3450)
at java.util.regex.Pattern.compile(Pattern.java:1716)
at java.util.regex.Pattern.(Pattern.java:1351)
at java.util.regex.Pattern.compile(Pattern.java:1028)
at java.lang.String.split(String.java:2380)
at java.lang.String.split(String.java:2422)
at htsjdk.samtools.filter.ReadNameFilter.(ReadNameFilter.java:58)
at picard.sam.FilterSamReads.doWork(FilterSamReads.java:233)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @Yingya,

    The combination of these two documents should help you determine the memory available on your system and the memory use of processes from the GATK Best Practices. I know these don't talk about FilterSamReads specifically but they can serve as general guidelines in memory similar processes would require. For example, I imagine FilterSamReads would be similar in memory requirement to GATK's PrintReads.

    • To determine memory available on your system, take a look at instructions in section 2 of this document.
    • For memory use of GATK tools, see Blog#7249's CPU utilization chart. There is a link to an updated Intel white paper in Blog#8605 with a similar utilization chart.

    I hope these are helpful.

Sign In or Register to comment.