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Mafft on Biowulf

MAFFT is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.

Running an interactive job

Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.


biowulf $ qsub -I -l nodes=1:g24:c24
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready

[user@pXXX]$ module load mafft
        
[user@pXXX]$ cd /data/$USER/XXXX

[user@pXXX]$ mafft input1 > output1
[user@pXXX]$ exit
qsub: job 2236960.biobos completed
user@biowulf]$ 

Submitting a single batch job

1. Create a script file along with the lines below. Modify the path of location before running.

2.

#!/bin/bash
# This file is runMafft
#
#PBS -N mafft
#PBS -m be
#PBS -k oe
module load mafft
cd /data/$USER/run1
mafft input1 > output1

3. Submit the script using the 'qsub' command on Biowulf

$ qsub -l nodes=1:g8 /data/$USER/runMafft

 

Submitting a swarm of jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:

cd /data/$USER/run1; mafft input1 > output1
cd /data/$USER/run2; mafft input1 > output1
........ ........ cd /data/$USER/run20; mafft input1 > output1

The '-f' and '--module' options for swarm are required

By default, each line of the command file above will be executed on 1 processor core of a node and use 1gb of memory. If this is not what you want, you will need to specify '-t' and '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

biowulf> $ swarm -g 10 -f cmdfile --module mafft

For more information regarding running swarm, see swarm.html

Documentation

http://mafft.cbrc.jp/alignment/software/