MAFFT-7.402¶
Basic Information¶
- Deploy date: 27 July 2018
- Official Website: https://mafft.cbrc.jp/alignment/software/
- License: BSD License
- Extensions:
- Mxcarna: BSD License (For more information check README file in
mafft-7.402-with-extensions/extensions/mxscarna_src/
- Foldalign: GNU GPL-2
- Contrafold: BSD License
- Mxcarna: BSD License (For more information check README file in
- Extensions:
- Installed on: Apolo II, Cronos
Installation¶
This entry covers the entire process performed for the installation and configuration of MAFFT with extensions (MXSCARNA, Foldalign and CONTRAfold) on a cluster.
Usage¶
This section describes the method to submit jobs with the resource manager SLURM.
Load the necessary environment.
module load mafft/7.402-with-extensions_intel-X.X.X
Note
Remember to load the proper environment for Cronos or Apolo
- Apolo
module load mafft/7.402-with-extensions_intel-17.0.1
- Cronos
module load mafft/7.402-with-extensions_intel-18.0.2
Run MAFFT with SLURM.
An example:
Note
This example was tested with
example.fa
that contains unlined DNA secuences.#!/bin/bash #SBATCH --partition=longjobs #SBATCH --nodes=1 #SBATCH --ntasks-per-node=32 #SBATCH --time=120:00:00 #SBATCH --job-name=test #SBATCH -o result_%N_%j.out # File to which STDOUT will be written #SBATCH -e result_%N_%j.err # File to which STDERR will be written #SBATCH --mail-type=ALL #SBATCH --mail-user=test@example.com export SBATCH_EXPORT=NONE export OMP_NUM_THREADS=1 mafft --quiet --auto --thread $SLURM_NTASKS example.fa > example_al.fa
Options
quiet
→ Do not report progress and this flag is mandatory to run unattended jobs.auto
→ Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size.thread
→ Number of threads (number of cores reserved on SLURM).
Note
For more information, please read the manual entry for Mafft
man mafft
ormafft -h
Authors¶
- Manuela Carrasco Pinzón <mcarras1@eafit.edu.co>