error, while running

[surendraphd]

Hi,
I am facing the following error, while running the job via command line.

FileNotFoundError: [Errno 2] No such file or directory: '/home/medicina/Downloads/DynamicBind/workdir/big_score_model_sanyueqi_with_time/pro_ema_inference_epoch138_model.pt'

my workdir contain only this file.

ema_inference_epoch314_model.pt

How to fix the issue.

(dynamicbind) medicina@medicina:~/Downloads/DynamicBind$ python run_single_protein_inference.py 1qg8_cleaned.pdb 1qg8_input.csv --savings_per_complex 40 --inference_steps 20 --header test --python /home/medicina/anaconda3/envs/dynamicbind/bin/python --relax_python /home/medicina/anaconda3/envs/relax/bin/python
INFO:root:run_single_protein_inference.py 1qg8_cleaned.pdb 1qg8_input.csv --savings_per_complex 40 --inference_steps 20 --header test --python /home/medicina/anaconda3/envs/dynamicbind/bin/python --relax_python /home/medicina/anaconda3/envs/relax/bin/python
2023_12_31_19_07

/home/medicina/Downloads/DynamicBind/run_single_protein_inference.py /home/medicina/Downloads/DynamicBind
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 59.60it/s]
hub dir /home/medicina/Downloads/DynamicBind/esm_models
Downloading: "https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t33_650M_UR50D.pt" to /home/medicina/Downloads/DynamicBind/esm_models/checkpoints/esm2_t33_650M_UR50D.pt
Downloading: "https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t33_650M_UR50D-contact-regression.pt" to /home/medicina/Downloads/DynamicBind/esm_models/checkpoints/esm2_t33_650M_UR50D-contact-regression.pt
Transferred model to GPU
Read data/prepared_for_esm_test.fasta with 1 sequences
Processing 1 of 1 batches (1 sequences)
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 201/201 [00:52<00:00, 3.80it/s]
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 201/201 [01:04<00:00, 3.13it/s]
Reading molecules and generating local structures with RDKit
4it [00:00, 14.83it/s]
Reading language model embeddings.
Generating graphs for ligands and proteins
loading complexes: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:00<00:00, 6.33it/s]
loading data from memory: data/cache_torsion/limit0_INDEX_maxLigSizeNone_H0_recRad15.0_recMax24_esmEmbeddings3297976096/heterographs.pkl
Number of complexes: 4
radius protein: mean 27.280357360839844, std 0.0, max 27.280357360839844
radius molecule: mean 6.446958541870117, std 0.2975179851055145, max 6.782521724700928
distance protein-mol: mean 5.086441845492118e-08, std 2.719834313325009e-08, max 9.765030029029731e-08
rmsd matching: mean 0.0, std 0.0, max 0
Traceback (most recent call last):
File "/home/medicina/Downloads/DynamicBind/inference.py", line 152, in
state_dict = torch.load(f'{args.model_dir}/{args.ckpt}', map_location=torch.device('cpu'))
File "/home/medicina/anaconda3/envs/dynamicbind/lib/python3.10/site-packages/torch/serialization.py", line 791, in load
with _open_file_like(f, 'rb') as opened_file:
File "/home/medicina/anaconda3/envs/dynamicbind/lib/python3.10/site-packages/torch/serialization.py", line 271, in _open_file_like
return _open_file(name_or_buffer, mode)
File "/home/medicina/anaconda3/envs/dynamicbind/lib/python3.10/site-packages/torch/serialization.py", line 252, in init
super().init(open(name, mode))
FileNotFoundError: [Errno 2] No such file or directory: '/home/medicina/Downloads/DynamicBind/workdir/big_score_model_sanyueqi_with_time/pro_ema_inference_epoch138_model.pt'
inference complete.
0it [00:00, ?it/s]
final step structure relax complete.

Thanks in advance.

[Nobody-Zhang]

You can fix this problem by just adding "-p" in your command line.
By referring to the file named "run_single_protein_inference.py", line 42, you can see why this arg fix it.