#!/usr/bin/env bash
#SBATCH --nodes=1            # Number of nodes
#SBATCH --ntasks-per-node=1  # Number of tasks per node
#SBATCH --cpus-per-task=10   # Number of OpenMP threads per task
#SBATCH --gpus-per-node=1    # Number of GPUs per node
#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 100h for V100, 20h for A100)
##
## Please, refer to comments below for 
## more information about these 4 last options.
##SBATCH --account=<account>@gpu       # 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
##SBATCH --qos=qos_gpu-t4      # Uncomment for job requiring more than 20h (max 16 GPU, V100 only)

module purge
module load alphafold/2.2.4
export TMP=$JOBSCRATCH
export TMPDIR=$JOBSCRATCH

## In this example we let the structures relax with OpenMM

python3 $(which run_alphafold.py) \                                                                                                                                                                               
    --output_dir=outputs \
    --uniref90_database_path=${DSDIR}/AlphaFold/uniref90/uniref90.fasta \
    --mgnify_database_path=${DSDIR}/AlphaFold/mgnify/mgy_clusters_2018_12.fa \
    --template_mmcif_dir=${DSDIR}/AlphaFold/pdb_mmcif/mmcif_files \
    --obsolete_pdbs_path=${DSDIR}/AlphaFold/pdb_mmcif/obsolete.dat \
    --bfd_database_path=${DSDIR}/AlphaFold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
    --pdb_seqres_database_path=${DSDIR}/AlphaFold/pdb_seqres/pdb_seqres.txt \
    --uniclust30_database_path=${DSDIR}/AlphaFold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
    --uniprot_database_path=${DSDIR}/AlphaFold/uniprot/uniprot.fasta \
    --use_gpu_relax \
    --model_preset=multimer \
    --fasta_paths=test.fasta \
    --max_template_date=2022-01-01 \
    --data_dir=${DSDIR}/AlphaFold/model_parameters/2.2.4