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 < ~30000 sequences), etc

References:

• https://academic.oup.com/nar/article/30/14/3059/2904316/

• https://mafft.cbrc.jp/alignment/software/

• Module Name: mafft (see the modules page for more information)
• Multithreaded
• Example files in MAFFT_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mafft
[user@cn3144 ~]$ mafft --thread $SLURM_CPUS_PER_TASK $MAFFT_TEST_DATA/ex1 > outfile
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load mafft
mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile
cd dir2; mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile
cd dir3; mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile
cd dir4; mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile

Submit this job using the swarm command.

swarm -f job.swarm [-g #] -t 4 --module mafft