#!/bin/bash
#SBATCH --job-name=alphafold
#SBATCH --time=04:00:00
#SBATCH --partition=regular
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=16GB

# Clean the module environment and load the squashfuse and AlphaFold module
module purge
module load AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0

# Uncomment the following line(s) if you want to use different values for the number of cores used by hhblits/jackhmmer
#export ALPHAFOLD_HHBLITS_N_CPU=8 # default: 4
#export ALPHAFOLD_JACKHMMER_N_CPU=4 # default: 8

# Use the CPU instead of a GPU
export OPENMM_RELAX=CPU

# Copy the squashfs image to $TMPDIR
cp /scratch/public/AlphaFold/2.3.1.zstd.sqsh $TMPDIR

# Create a mountpoint for the AlphaFold database in squashfs format
mkdir $TMPDIR/alphafold_data
# Mount the AlphaFold database squashfs image
squashfuse $TMPDIR/2.3.1.zstd.sqsh $TMPDIR/alphafold_data
# Set the path to the AlphaFold database
export ALPHAFOLD_DATA_DIR=$TMPDIR/alphafold_data

# Run AlphaFold
alphafold --fasta_paths=query.fasta --max_template_date=2020-05-14 --output_dir=output

# Unmount the database image
fusermount -u $TMPDIR/alphafold_data