From ceb5aa1ca3a5554568b54f8578a1fe16cd8a70a8 Mon Sep 17 00:00:00 2001 From: jyaacoub Date: Mon, 31 Jul 2023 11:27:34 -0400 Subject: [PATCH] fix(docking): path issues in `multi_dock.sh` --- src/docking/sbatch/multi_dock.sh | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/docking/sbatch/multi_dock.sh b/src/docking/sbatch/multi_dock.sh index aa700a8d..4ea7a316 100755 --- a/src/docking/sbatch/multi_dock.sh +++ b/src/docking/sbatch/multi_dock.sh @@ -1,5 +1,5 @@ #!/bin/bash -#SBATCH -t 1-00:00:00 #days-hours:minutes:seconds +#SBATCH -t 2-00:00:00 #days-hours:minutes:seconds #SBATCH -o /cluster/projects/kumargroup/jean/slurm-outputs/docking/run11/%x-%A_%a.out #NOTE: change run# #SBATCH --job-name=r11_vina_dock #NOTE: change run# @@ -7,9 +7,9 @@ ##SBATCH --mail-user=j.yaacoub@mail.utoronto.ca #SBATCH --mem=4G -#SBATCH --cpus-per-task=4 +#SBATCH --cpus-per-task=8 -#SBATCH --array=0 #NOTE: N total processes +#SBATCH --array=0-40 #NOTE: N total processes # takes ~1.5 days on 5 process nodes with 3,000 pdbs # adding needed libraries to path: @@ -30,13 +30,14 @@ echo "run_num: $run_num" # e.g.: vina --config /cluster/projects/kumargroup/jean/data/refined-set/1a1e/1a1e_conf.txt --seed 904455071 # shortlist file is different for each job in the array conf_dir="/cluster/projects/kumargroup/jean/data/vina_conf/run${run_num}/" -shortlist=/cluster/projects/kumargroup/jean/data/shortlists/kd_ki/${SLURM_ARRAY_TASK_ID}.csv -run_vina=/cluster/home/t122995uhn/projects/MutDTA/src/docking/bash_scripts/run_vina.sh -pdb_data="/cluster/projects/kumargroup/jean/data/refined-set/" +shortlist=/cluster/projects/kumargroup/jean/data/shortlists/refined-set/${SLURM_ARRAY_TASK_ID}.csv +vina=/cluster/home/t122995uhn/projects/MutDTA/src/docking/bash_scripts/run_vina.sh +data="/cluster/projects/kumargroup/jean/data/refined-set/" echo "shortlist: $shortlist" echo "conf_dir: $conf_dir" +echo "data: $data" -$run_vina $pdb_data $shortlist $conf_dir +$vina $data $shortlist $conf_dir # Then extract with `extract_vina_out.py`