Merlin on Biowulf

MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around (Abecasis et al, 2002).

Submitting Merlin jobs

1. First log in to your biowulf account.

2. For basic information about setting up an Merlin job, see below. Also see the Batch Queuing System in the Biowulf user guide.

3. Create a script file. The file will contain the lines similar to the lines below between dotted lines. Modify the name of the file on line2 and the command on last line to fit your needs:

 The sample script file can be saved as /home/username/runMerlin

..................................................................
#!/bin/tcsh
# This file is runMerlin
#
#PBS -N merlin
#PBS -m be
#PBS -k oe
date
/usr/local/bin/merlin -d c1.dat -m c1.map -p simdata --quiet
..................................................................

4. Submit the script using the 'qsub' command, e.g.

qsub -v -l nodes=1 /home/username/runMerlin

Running a 'swarm' of Merlin jobs

The swarm program is a convenient way to submit large numbers of jobs all at once instead of manually submit them one by one.

1. Create a swarm command file containing a single job on each line, e.g.

    The sample swarm command file is called /home/username/merlinjobs
    .................................................................
    /usr/local/bin/merlin -d c1.dat -m c1.map -p simdata --quiet
    /usr/local/bin/merlin -d c2.dat -m c2.map -p simdata --quiet
    /usr/local/bin/merlin -d c3.dat -m c3.map -p simdata --quiet
    /usr/local/bin/merlin -d c4.dat -m c4.map -p simdata --quiet
    /usr/local/bin/merlin -d c5.dat -m c5.map -p simdata --quiet
    Add as many lines as needed
    .................................................................
			

2. Submit this swarm job by typing:

    swarm -f /home/username/merlinjobs 

3  Swarm will run 2 jobs per node, since the Biowulf nodes are all 2-processor. See the Swarm documentation for more information.

Documentation

http://csg.sph.umich.edu/pn/index.php?furl=/abecasis/Merlin/