#!/bin/bash

input_file="<provide_user_dir>"
sensitivity=7.5
coverage=0.5
cov_mode=1
alignment_mode=3
alignment_output_mode=0
evalue=0.001
min_seq_id=0
seq_id_mode=0
cluster_mode=1
output_dir="<provide_user_output_dir>"
threads=64

python code/run_mmseqs.py \
        -i  $input_file \
        -o $output_dir \
        -s $sensitivity \
        -c $coverage \
        --cov_mode $cov_mode \
        --alignment_mode $alignment_mode \
        --alignment_output_mode $alignment_output_mode \
        -e $evalue \
        --min_seq_id $min_seq_id \
        --seq_id_mode $seq_id_mode \
        --cluster_mode $cluster_mode \
        --create_db \
        --prefilter \
        --align \
        --threads $threads \
        -v 3 \