MAFFT: Difference between revisions
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[https://mafft.cbrc.jp/alignment/software/ 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 <∼30,000 sequences), etc. | [https://mafft.cbrc.jp/alignment/software/ 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 <∼30,000 sequences), etc. | ||
== Single node == | == Single node == <!--T:2--> | ||
MAFFT can benefit from multiple cores on a single node. For more information: https://mafft.cbrc.jp/alignment/software/multithreading.html | MAFFT can benefit from multiple cores on a single node. For more information: https://mafft.cbrc.jp/alignment/software/multithreading.html | ||
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'''Note''': The <tt>MAFFT_TMPDIR</tt> is set to <tt>$SLURM_TMPDIR/maffttmp</tt> when you load the module. | '''Note''': The <tt>MAFFT_TMPDIR</tt> is set to <tt>$SLURM_TMPDIR/maffttmp</tt> when you load the module. | ||
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{{File | {{File | ||
|name=mafft_submit.sh | |name=mafft_submit.sh | ||
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#!/bin/bash | #!/bin/bash | ||
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#SBATCH --time=24:00:00 | #SBATCH --time=24:00:00 | ||
#SBATCH --nodes=1 | #SBATCH --nodes=1 | ||
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#SBATCH --mem=0 | #SBATCH --mem=0 | ||
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module load gcc/9.3.0 mafft | module load gcc/9.3.0 mafft | ||
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mafft --globalpair --thread $SLURM_CPUS_PER_TASK input > output | mafft --globalpair --thread $SLURM_CPUS_PER_TASK input > output | ||
}} | }} | ||
== Multiple nodes (MPI) == | == Multiple nodes (MPI) == <!--T:8--> | ||
MAFFT can use MPI to align a large number of sequences: https://mafft.cbrc.jp/alignment/software/mpi.html | MAFFT can use MPI to align a large number of sequences: https://mafft.cbrc.jp/alignment/software/mpi.html | ||
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'''Note''': <tt>MAFFT_TMPDIR</tt> is set to <tt>$SCRATCH/maffttmp</tt> when you load the module. | '''Note''': <tt>MAFFT_TMPDIR</tt> is set to <tt>$SCRATCH/maffttmp</tt> when you load the module. | ||
If you change this temporary directory, it must be shared by all hosts. | If you change this temporary directory, it must be shared by all hosts. | ||
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{{File | {{File | ||
|name=mafft_mpi_submit.sh | |name=mafft_mpi_submit.sh | ||
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#!/bin/bash | #!/bin/bash | ||
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#SBATCH --time=04:00:00 | #SBATCH --time=04:00:00 | ||
#SBATCH --nodes=2 | #SBATCH --nodes=2 | ||
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#SBATCH --mem=12G | #SBATCH --mem=12G | ||
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module load gcc/9.3.0 mafft-mpi | module load gcc/9.3.0 mafft-mpi | ||
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srun mafft --mpi --large --globalpair --thread $SLURM_CPUS_PER_TASK input > output | srun mafft --mpi --large --globalpair --thread $SLURM_CPUS_PER_TASK input > output | ||
}} | }} | ||
</translate> | </translate> | ||
Latest revision as of 15:35, 29 July 2020
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 <∼30,000 sequences), etc.
Single node[edit]
MAFFT can benefit from multiple cores on a single node. For more information: https://mafft.cbrc.jp/alignment/software/multithreading.html
Note: The MAFFT_TMPDIR is set to $SLURM_TMPDIR/maffttmp when you load the module.
File : mafft_submit.sh
#!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=0
module load gcc/9.3.0 mafft
mafft --globalpair --thread $SLURM_CPUS_PER_TASK input > output
Multiple nodes (MPI)[edit]
MAFFT can use MPI to align a large number of sequences: https://mafft.cbrc.jp/alignment/software/mpi.html
Note: MAFFT_TMPDIR is set to $SCRATCH/maffttmp when you load the module. If you change this temporary directory, it must be shared by all hosts.
File : mafft_mpi_submit.sh
#!/bin/bash
#SBATCH --time=04:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --mem=12G
module load gcc/9.3.0 mafft-mpi
srun mafft --mpi --large --globalpair --thread $SLURM_CPUS_PER_TASK input > output