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bigginlab / ABFE_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
GNU General Public License v3.0
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Enhancement: Should add output flag to the submission script #18

Closed Nithishwer closed 1 year ago

Nithishwer commented 1 year ago

When I ran example execution.sh with bash, I got an error saying that:

Traceback (most recent call last): File "/biggin/b211/reub0138/mambaforge/envs/abfe/bin/cli-abfe", line 16, in sys.exit(main()) File "/biggin/b211/reub0138/Projects/abfe/IrfansPaper/ABFE_workflow-main/abfe_cli/ABFECalculator.py", line 56, in main res = calculate_abfe(protein_pdb_path=args.protein_pdb_path, ligand_sdf_paths=sdf_paths, out_root_folder_path=args.output_dir_path, File "/biggin/b211/reub0138/Projects/abfe/IrfansPaper/ABFE_workflow-main/abfe/calculate_abfe.py", line 32, in calculate_abfe os.mkdir(dir_path).

FileNotFoundError: [Errno 2] No such file or directory: '***/CyclophilinD_selfParametrized'

This is because the output directory was unspecified. Therefore, I had to add the following to the cli-abfe call in the submission script:

      -o /biggin/b211/reub0138/Projects/abfe/IrfansPaper/ABFE_workflow-main/examples/out

This seemed to fix the issue

RiesBen commented 1 year ago

good catch! Fixed.