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compute_msa.sh
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compute_msa.sh
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#!/bin/bash
#SBATCH --job-name=msa-compute
#SBATCH --time=16:00:00
#SBATCH --mem-per-cpu=16GB
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=2
input=$1 #Fasta file path: $1
output=$2 #Output directory: $2
run_parafold_path=$3 #path to run_alphafold.sh script in the parallelfold installation
dbpath=$4 #directory to alphafold database folder
i=$5 #index of input fasta file
paths=$6 #concatenated string of path to each database file split by ";", see compute_msa_parallel.sh file for ordering
installation_dir=$7
echo $installation_dir
filename=$(basename -- "$input")
gene="${filename%.*}"
date=$(date +"%Y-%m-%d")
log="${date}_${gene}_precomputed_log.txt"
log=$output"/"$log
echo "Started MSA Computation:"$(date +"%Y-%m-%d %T") > $log
bash $run_parafold_path \
-a $installation_dir \
-d $dbpath \
-b $paths \
-o $output \
-p multimer \
-i $input \
-f true \
-m model_1_multimer_v2 \
-t 1800-01-01 \
-c reduced_dbs \
-use_gpu_relax=false
echo "Finished MSA Computation:"$(date +"%Y-%m-%d %T") >> $log