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mafft_MSA.pbs
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mafft_MSA.pbs
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#!/usr/bin/env bash
#PBS -q omp
#PBS -l ncpus=16
#PBS -l mem=110gb
#PBS -l walltime=05:00:00
## DESCRIPTION ##
# Metagenomics analysis targeted viral reads
## USAGE ##
# qsub -v "outdir=,MSNA=,output=msa_mafft_dna.fna" /home1/datawork/jdelmott/Hemovir/src/mafft_MSNA.pbs
## History ##
# 2020-03-29 Creation du programme
################################ Execute script ################################
export PATH=/appli/anaconda/3.7/bin/:$PATH
source activate /home1/datahome/jdelmott/conda-env/mafft
cd $outdir
logfile=mafft_logFile.txt
echo -e "Commande : ${0}" > $logfile
echo -e "Start at : $(date +%Y-%m-%d_%Hh%Mm%Ss)\n" >> $logfile
echo -e "outdir=${outdir}" >> $logfile
echo -e "MSNA=${MSNA}" >> $logfile
echo -e "output=${output}\n" >> $logfile
if [ ! -f $output ]
then
echo -e '\n Multiple Sequence Alignment... \n' >> $logfile
mafft \
--thread $NCPUS \
--auto \
$MSNA \
> $output \
2>> $logfile
# --ep 0.15 \
else
echo -e '\n Multiple Sequence Alignment already exist' >> $logfile
fi