MAFFT

#!/bin/bash
#SBATCH -p compute      # specific partition (compute,memory)
#SBATCH -N 1 -c 16      # -N 1 must be 1, -c can be 16, 32, 64, 128 depending on the requirement
#SBATCH -t 02:00:00     # job time limit <hr:min:sec>
#SBATCH -A lt200xxx     # project ID      
#SBATCH -J MAFFT        # job name

module restore
module load MAFFT/7.505-cpeGNU-23.03-with-extensions

#Set TMPDIR location, uncomment and modify projectID-shortname 
#mkdir -p /scratch/lt200xxx-abcdef/$USER/$SLURM_JOB_ID
#export MAFFT_TMPDIR=/scratch/lt200xxx-abcdef/$USER/$SLURM_JOB_ID

mafft --thread $SLURM_CPUS_PER_TASK --threadtb 16 --threadit 16 input.fasta > aligned.fasta

#!/bin/bash
#SBATCH -p memory         # specific partition (compute,memory)
#SBATCH -N 2 --ntasks-per-node=1 -c 128    # specify computing resources ( 2 nodes, 1 task per node, 128 threads per task)
#SBATCH -t 02:00:00       # job time limit <hr:min:sec>
#SBATCH -A lt200xxx       # project name
#SBATCH -J MAFFT128-mpi   # job name

module restore
module load MAFFT/7.505-cpeGNU-23.03-with-extensions

# set enviroment variable according to https://mafft.cbrc.jp/alignment/software/mpi.html
export MAFFT_MPIRUN="srun"
export MAFFT_N_THREADS_PER_PROCESS="128"

#Set TMPDIR location, uncomment and modify projectID-shortname 
#mkdir -p /scratch/lt200xxx-abcdef/$USER/$SLURM_JOB_ID
#export MAFFT_TMPDIR=/scratch/lt200xxx-abcdef/$USER/$SLURM_JOB_ID

# Run the script to be monitored
mafft --mpi --large --thread $SLURM_CPUS_PER_TASK input.fasta > aligned.fasta