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  • Question about haplotype phasing by BEAGLE

    Dear all

    I am doing the haplotype phasing by BEAGLE. But the output file is 0 byte.

    Here is the malformation form the Terminal.

    [user@user BEAGLE3.3.2]$ java -Xmx1000m -jar beagle.jar unphased=/home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/genome_user_for_BEAGLE.txt missing=- out=/home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/genome_user_for_BEAGLE_phased.txt > /home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/log.txt
    Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at phaser.ai.<init>(Unknown Source)
    at phaser.w.<init>(Unknown Source)
    at phaser.S.a(Unknown Source)
    at phaser.ae.a(Unknown Source)
    at phaser.PhaseMain.<init>(Unknown Source)
    at phaser.PhaseMain.main(Unknown Source)


    And here is the log information

    Beagle version 3.3.2 (31 Oct 2011)
    Enter "java -jar beagle.jar" for summary of command line arguments.
    Start time: 04:54 PM EST on 04 Feb 2014

    Command line: java -Xmx888m -jar beagle.jar
    unphased=/home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/genome_user_for_BEAGLE.txt
    missing=-
    out=/home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/genome_user_for_BEAGLE_phased.txt

    number of markers = 912737
    number of haplotypes = 2 (genome_user_for_BEAGLE.txt)

    The input file format is like this.
    M rs8178835 G G
    M rs17769593 A A
    M rs1801692 C C
    M rs3826358 A A
    M rs8178822 G G
    M rs8178899 T T
    M rs3760292 - -
    M rs8178819 C C
    M rs17769836 G G
    M rs7206973 G G
    M rs10048158 C C
    M rs2013785 G G

    I don't know what's wrong with this. Please help me.

    Thank you in advance

  • #2
    some one can help me?

    Comment


    • #3
      Hi ..

      u ned to specify temp directory to fix it

      java -Djava.io.tmpdir=/home/temp/ -Xmx1000m -jar beagle.jar unphased=/home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/genome_user_for_BEAGLE.txt missing=- out=/home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/genome_user_for_BEAGLE_phased.txt > /home/user/Documents/user/BEAGLE3.3.2/genome_user_Full/log.txt


      cheers

      Comment

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