PBAT: Tools for the statistical analysis of family-based association studies (FBAT), developed by Christoph Lange.

PBAT is not a parallel program. Single PBAT jobs should be run interactively on the Biowulf interactive nodes or Helix. If you have multiple PBAT jobs to run, the swarm utility is recommended.

Below are sample sessions for three submission methods.

Swarm Sample Session:

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

1. First create different directories for each PBAT run. Put all the required input files under each of the created directories.

2. For each directory, create a script file which contains the PBAT commands.. Each line contains the command exactly like what you would enter when running interactively at the prompt. For example, under /data/user/pbat/run1 directory, a file called 'script1' was created and content of the file looks like below. Please note the blank lines in this file represent the 'enter' keys and is required as when prompted 'any key to clear screen' when running interactively:

cd /data/user/pabt/run1;/usr/local/bin/pbat <<EOF


1

1
1
1
0
213
1
1
2
1
175
0
1
1
3
1
175
0
1
1
2
2
220
0
1
1
3
2
220
0
1
3
test1
0
2
0
2
1
2
.1
1
.1
.05
0
3
0.01
0.1


4
1

4
2

4
3


4
3

-1
EOF

3. Now prepare the swarm command file. For example, a swam command file called 'cmdfile' contains the following lines:

/data/user/pbat/run1/script1
/data/user/pbat/run2/script2
/data/user/pbat/run3/script3
/data/user/pbat/run4/script4
.....
....
/data/user/pbat/runN/scriptN

4. Now submit the Swarm job

biowulf% swarm -f cmdfile

--- file pbat.script ----------
#!/bin/csh
#PBS -m be
#
cd /data/user/pabt/run1
/usr/local/bin/pbat <<EOF


1

1
1
1
0
213
1
1
2
1
175
0
1
1
3
1
175
0
1
1
2
2
220
0
1
1
3
2
220
0
1
3
test1
0
2
0
2
1
2
.1
1
.1
.05
0
3
0.01
0.1


4
1

4
2

4
3


4
3

-1
EOF

qsub -l nodes=1 /data/user/pbat/run1/script