Question about haplotype phasing by BEAGLE

[illuminaGA]

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

[illuminaGA]

some one can help me?

[jdc]

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