#!/usr/bin/env bash
#SBATCH --nodes=1            # Number of nodes
#SBATCH --ntasks-per-node=1  # Number of tasks per node
#SBATCH --cpus-per-task=8    # Number of OpenMP threads per task
#SBATCH --gpus-per-node=1    # Number of GPUs per node
#SBATCH -C a100              # Use A100 partition
#SBATCH --hint=nomultithread # Disable hyperthreading
#SBATCH --job-name=alphafold # Jobname
#SBATCH --output=%x.o%j      # Output file %x is the jobname, %j the jobid
#SBATCH --error=%x.o%j       # Error file
#SBATCH --time=10:00:00      # Expected runtime HH:MM:SS (max 20h)
##
## Please, refer to comments below for 
## more information about these 3 last options.
##SBATCH --account=<account>@a100      # To specify cpu accounting: <account> = echo $IDRPROJ
##SBATCH --partition=<partition>       # To specify partition (see IDRIS web site for more info)
##SBATCH --qos=qos_gpu-dev             # Uncomment for job requiring less than 2 hours                                                                                                                                                               

module purge
module load cpuarch/amd
module load alphafold/2.3.1
export TMP=$JOBSCRATCH
export TMPDIR=$JOBSCRATCH

fafile=test.fa

python3 $(which run_alphafold.py) \
    --output_dir=outputs_${fafile} \
    --uniref90_database_path=${ALPHAFOLDDB}/uniref90/uniref90.fasta \
    --mgnify_database_path=${ALPHAFOLDDB}/mgnify/mgy_clusters_2022_05.fa \
    --template_mmcif_dir=${ALPHAFOLDDB}/pdb_mmcif \
    --obsolete_pdbs_path=${ALPHAFOLDDB}/pdb_mmcif/obsolete.dat \
    --bfd_database_path=${ALPHAFOLDDB}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
    --pdb70_database_path=${ALPHAFOLDDB}/pdb70/pdb70 \
    --uniref30_database_path=${ALPHAFOLDDB}/uniref30/UniRef30_2021_03 \
    --use_gpu_relax \
    --model_preset=monomer \
    --fasta_paths=${fafile} \
    --max_template_date=2022-01-01 \
    --data_dir=${ALPHAFOLDDB}/model_parameters/2.3.1