#!/bin/bash

input_folder="<provide_user_dir>"
tm_thresh=0
tmalign_hit_order=0
tmalign_fast=1
lddt_threshold=0
alignment_type=1
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
use_easy=False
threads=64
output_dir="<provide_user_output_dir>"

python code/run_foldseek.py \
        -i  $input_folder \
        -o $output_dir \
        --tm_thresh $tm_thresh \
        --tmalign_hit_order $tmalign_hit_order \
        --tmalign_fast $tmalign_fast \
        --lddt_threshold $lddt_threshold \
        --alignment_type $alignment_type \
        -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 \
        --use_easy $use_easy \
        --create_db \
        --search \
        --threads $threads \
        -v 3 \