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DeepRank / DeepRank-GNN-esm

Graph Network for protein-protein interface including language model features
Apache License 2.0
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Why cannot generate the CSV #5

Open Luckken21 opened 1 month ago

Luckken21 commented 1 month ago

/gpfs/share/home/2200012187/mambaforge/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage() storage = elem.storage()._new_shared(numel) Traceback (most recent call last): File "/gpfs/share/home/2200012187/mambaforge/envs/deeprank-gnn-esm-gpu/bin/deeprank-gnn-esm-predict", line 8, in sys.exit(main()) File "/gpfs/share/home/2200012187/mambaforge/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 340, in main csv_output = predict(input=graph, workspace_path=workspace_path) File "/gpfs/share/home/2200012187/mambaforge/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 264, in predict output_csv = convert_to_csv(output) File "/gpfs/share/home/2200012187/mambaforge/envs/deeprank-gnn-esm-gpu/lib/python3.9/site-packages/deeprank_gnn/predict.py", line 274, in convert_to_csv assert os.path.exists(csv_path), f"CSV file {csv_path} not found." AssertionError: CSV file /gpfs/share/home/2200012187/lightdock_workspace/DeepRank-GNN-esm/lightdock_100_82.pdb_design_cdc42_323_dldesign_2_2_af2pred_cleaned-gnn_esm_pred_A_B/GNN_esm_prediction.csv not found. I successfully run another pdb, but for this , the program cannot generate the csv. Thanks a lot if you can help me

ntxxt commented 1 month ago

Hi there,

For this pdb, in the output folder, do you have the generated '/gpfs/share/home/2200012187/lightdock_workspace/DeepRank-GNN-esm/lightdock_100_82.pdb_design_cdc42_323_dldesign_2_2_af2pred_cleaned-gnn_esm_pred_A_B/GNN_esm_prediction.hdf5' file? If so, try use 'https://github.com/DeepRank/DeepRank-GNN-esm/blob/main/src/deeprank_gnn/tools/hdf5_to_csv.py' script directly to convert it into hdf5 format; If not, check the following 1) search for the GNN_esm_prediction.hdf5 file in the output dir, it could be a naming issue 2) check if your input pdb has chain 'A' and 'B' and if the input pdb has been properly cleaned and pre-processed. (should be you use the command-line version of the tool)

If is it still not solved, could you paste all of the output from the cmd tool for this input pdb so that I can have a detailed look?

Best, Xiaotong