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

  • 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.

  1. 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

  2. Run MAFFT with SLURM.

    An example:

    Note

    This example was tested with example.fa that contains unlined DNA secuences.

    mafft.sh
    #!/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 or mafft -h

Authors