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.
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]$
1. Create a script file along with the lines below. Modify the path of location before running.
#!/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
- -f: the swarm command file name above (required)
- --module: load the preserves the environment variables for the swarm jobs
- -g: gb of memory needed for each line of the commands in the swarm file above.(optional)
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