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Bhattacharya-Lab / EquiPNAS

pLM-informed E(3) equivariant deep graph neural networks for protein-nucleic acid binding site prediction
GNU General Public License v3.0
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Unknown error uisng test data-set #1

Open kazumaxneo opened 3 months ago

kazumaxneo commented 3 months ago

Hello.

I want to use EquiPNAS to check my TF bing sites (picked up from RNA seq experiment). After creating the environment with conda, I downloaded the published models and tested the operation. However, anknown error occurred. Is there any solution?

git clone https://github.com/Bhattacharya-Lab/EquiPNAS.git cd EquiPNAS/ mamba env create -f EquiPNAS_env.yml conda activate EquiPNAS

Python version 3.10.4

$ python EquiPNAS.py --model_state_dict models/EquiPNAS-RNA/E-l12-768.pt --indir Preprocessing/ --outdir output/

Residie-level predictions for each target is being saved at output//

Traceback (most recent call last): File "/home/kazu/Documents/EquiPNAS/EquiPNAS.py", line 155, in main(PARS) File "/home/kazu/Documents/EquiPNAS/EquiPNAS.py", line 92, in main model.load_state_dict(torch.load(PARS.model_state_dict, map_location=device)) UnboundLocalError: local variable 'model' referenced before assignment (EquiPNAS) kazu@kazu:~/Documents/EquiPNAS$

Roche78 commented 3 months ago

From your output error:

File "/home/kazu/Documents/EquiPNAS/EquiPNAS.py", line 92, in main
model.load_state_dict(torch.load(PARS.model_state_dict, map_location=device))

However, line 92 of EquiPNAS.py in the main function is:

inference_loader = GraphDataLoader(dataset, batch_size=1, shuffle=False)

which is different from what you reported. Have you changed EquiPNAS.py? If so, these changes might be causing the error. Please try using the original EquiPNAS.py.

Please closely follow the installation and usage instructions