| # | |
| # Estimates couplings model from alignment with plmc package | |
| # | |
| #SBATCH --cluster=<clustername> | |
| #SBATCH --partition=<partitionname> | |
| #SBATCH --account=<accountname> | |
| #SBATCH --job-name=plmc | |
| #SBATCH --output=logs/plmc.out | |
| #SBATCH --gres=gpu:0 # Number of GPU(s) per node. | |
| #SBATCH --cpus-per-task=2 # CPU cores/threads | |
| #SBATCH --mem=4000M # memory per node | |
| #SBATCH --time=0-24:00 # Max time (DD-HH:MM) | |
| #SBATCH --ntasks=1 # Only set to >1 if you want to use multi-threading | |
| #export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK | |
| PROTEIN=$1 | |
| DATASET=$2 | |
| PLMC_DIR="$HOME" | |
| mkdir -p inference/$DATASET/plmc | |
| #$PLMC_DIR/plmc/bin/plmc \ | |
| /share/descartes/Users/gz2294/miniconda3/envs/protein_fitness_prediction/bin/plmc \ | |
| -o inference/$DATASET/plmc/uniref100.model_params \ | |
| -c inference/$DATASET/plmc/uniref100.EC \ | |
| -f $PROTEIN \ | |
| -le 16.2 -lh 0.01 -m 200 -t 0.2 \ | |
| -g msa/$PROTEIN.a2m | |