TypeError: 'NoneType' object is not subscriptable

[lake-chao]

I installed abfe_workflow, and picked one pdbbind entry, 3pe1, for test. When I ran using cli

cli-abfe -p 3pe1.pdb -l 3pe1_ligands -nr 3 -njr 8 -njl 8 -nosubmit -nogpu -nohybrid -o output

Unfortunately, I got following errors:

Prepare
starting preparing ABFE-ligand file structur
Ligand: ligand-1
Traceback (most recent call last):
File "/opt/conda/envs/abfe/bin/cli-abfe", line 8, in
sys.exit(main())
File "/opt/conda/envs/abfe/lib/python3.10/site-packages/abfe_cli/ABFECalculator.py", line 54, 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 "/opt/conda/envs/abfe/lib/python3.10/site-packages/abfe/calculate_abfe.py", line 45, in calculate_abfe
build_ligand_flows(input_ligand_paths=conf["input_ligands_sdf_path"],
File "/opt/conda/envs/abfe/lib/python3.10/site-packages/abfe/orchestration/build_ligand_flow.py", line 213, in build_ligand_flows
build_replicas_simulation_flow(out_ligand_path=out_ligand_path,
File "/opt/conda/envs/abfe/lib/python3.10/site-packages/abfe/orchestration/build_ligand_flow.py", line 179, in build_replicas_simulation_flow
_ = scheduler.generate_scheduler_file(out_prefix=f"{approach_name}_{ligand_rep_name}")
File "/opt/conda/envs/abfe/lib/python3.10/site-packages/abfe/orchestration/generate_scheduler.py", line 38, in generate_scheduler_file
cluster_config = copy.deepcopy(self.cluster_config["Snakemake_job"])

TypeError: 'NoneType' object is not subscriptable

Thank you.

[philbiggin]

@RiesBen - are you able to pick up?

[RiesBen]

Hi @lake-chao,
first time ever I see this, I have a bit of a packed week, but I try to look into this, this week.

[lake-chao]

Thank you so much. No hurry on this. I am just trying to get it work and see how it performs on pdbbind entries.

…

On Mon, Oct 28, 2024 at 7:58 AM Benjamin Ries ***@***.***> wrote: Hi @lake-chao <https://github.com/lake-chao>, first time ever I see this, I have a bit of a packed week, but I try to look into this, this week. — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARQXWCFNXTC5YI747X4L7WTZ5YKEZAVCNFSM6AAAAABQTI2KZ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINBRGM4DEMBWHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[lake-chao]

Hi Ben, I found a workaround for this issue near line 20 after self.def_cluster_config = json.load(open(f"{default_slurm_config_path}", "r")) in the file of abfe/orchestration/generate_scheduler.py replace self.cluster_config = cluster_config by self.cluster_config = self.def_cluster_config Basically, cluster_config is not defined before its use. After I "fixed" this issue, I ran into a number of other issues with snakemake. So far, I could not this command line work: cli-abfe -p 3pe1.pdb -l 3pe1_ligands -nr 3 -njr 8 -njl 1 -nosubmit -nohybrid -nogpu -o output Regards,

…

On Mon, Oct 28, 2024 at 7:58 AM Benjamin Ries ***@***.***> wrote: Hi @lake-chao <https://github.com/lake-chao>, first time ever I see this, I have a bit of a packed week, but I try to look into this, this week. — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARQXWCFNXTC5YI747X4L7WTZ5YKEZAVCNFSM6AAAAABQTI2KZ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINBRGM4DEMBWHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[RobertArbon]

Hi folks,

I've come across the same problem. When running with -nosubmit the the cluster configuration is None which, as @lake-chao points out means the Scheduler.generate_scheduler_file method can't run. Instead of their suggestion, i've changed how the nosbumit flag gets parsed in the cli, see #34