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Approach Two: submit one loop shell script

#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -cwd
#$ -o logfile
#$ -pe threaded 24
#export PATH=/scratch2/software/anaconda/bin:$PATH

while read line
do

mafft --auto --thread 24 /misc/scratch2/####/$line.fasta >/misc/scratch2/####/aligned/$line.aligned.fasta

/scratch2/software/anaconda/envs/bmge/bin/bmge -i /misc/scratch2/####/aligned/$line.aligned.fasta -t AA -m BLOSUM30 -of /misc/scratch2/xizhang/####/trimmed/$line.aligned.trimmed.fasta

FastTree /misc/scratch2/####/trimmed/$line.aligned.trimmed.fasta > /misc/scratch2/####/fasttree/$line.aligned.trimmed.newick

done <$1