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  • CATCH - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #687 ] Out of memory when reading large wig files
    Date:
    01/06/09 09:59
    Submitted by:
    glyn_dk
    Assigned to:
    glyn_dk
    Category:
    ALG file handling
    Priority:
    5
    Ticket group:
    reproducible
    Resolution:
    Resolved
    Summary:
    Out of memory when reading large wig files
    Original submission:
    - File -> Import files
    - add signal files (largest one is 62M)
    /home/catch1/Desktop/Barski_ChIPseq/hg18/CTCF.vstep
    /home/catch1/Desktop/Barski_ChIPseq/hg18/H2AZ.vstep
    /home/catch1/Desktop/Barski_ChIPseq/hg18/H2BK5me1.vstep
    /home/catch1/Desktop/Barski_ChIPseq/hg18/H3K27me1.vstep
    /home/catch1/Desktop/Barski_ChIPseq/hg18/H3K27me2.vstep
    /home/catch1/Desktop/Barski_ChIPseq/hg18/H3K27me3.vstep

    - add position files
    /home/catch1/Desktop/ENCODE regions/RefSeq_TSS_in_ENCODE_regions_hg17.bed

    - click 'Convert and add to CATCH'

    BUG: see console output below
    ...
    53738
    53739
    53740
    53741
    Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
    at java.util.regex.Matcher.<init>(Matcher.java:207)
    at java.util.regex.Pattern.matcher(Pattern.java:888)
    at fileControllers.TrackUtils.readvarwiggletrack(TrackUtils.java:166)
    at fileControllers.TrackUtils.linematcher(TrackUtils.java:123)
    at fileControllers.TrackUtils.readwiggletrack(TrackUtils.java:84)
    at fileControllers.ExtractWiggleLines.extractwigglelines(ExtractWiggleLines.java:85)
    at fileControllers.ExtractWiggleLines.conversionPartOne(ExtractWiggleLines.java:49)
    at fileControllers.ExtractWiggleLines.conversionstepone(ExtractWiggleLines.java:40)
    at fileControllers.ExtractWiggleLines.conversionstepone(ExtractWiggleLines.java:26)
    at fileManager.FileInterfaceGui.convert(FileInterfaceGui.java:368)
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    Heap size can be extended by running CATCH from the commandline with extra options for the JVM, e.g. to set max heap size to 1GB:

    java -Xms1000M -Xmx1000M -jar CATCH3.jar &

    For more information on Java heap settings, read:
    http://www.caucho.com/resin-3.0/performance/jvm-tuning.xtp
    01/11/09 08:56 glyn_dk
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Unset 01/11/09 08:56 glyn_dk
    assigned_to unset 01/11/09 08:56 glyn_dk
    resolution_id Unset 01/11/09 08:56 glyn_dk
    close_date 12/31/69 19:00 01/11/09 08:56 glyn_dk

     

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