| [Errno 2] No such file or directory: '/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/release_data/ccd_cache/components.v20240608.cif': | |
| Traceback (most recent call last): | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/infer_data_pipeline.py", line 211, in __getitem__ | |
| data, atom_array, _ = self.process_one( | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/infer_data_pipeline.py", line 101, in process_one | |
| sample2feat = SampleDictToFeatures( | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_to_feature.py", line 34, in __init__ | |
| self.input_dict = add_entity_atom_array(single_sample_dict) | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_parser.py", line 605, in add_entity_atom_array | |
| atom_info = build_polymer(entity_info) | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_parser.py", line 345, in build_polymer | |
| chain_array = _build_polymer_atom_array(ccd_seqs) | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_parser.py", line 290, in _build_polymer_atom_array | |
| residue = ccd.get_component_atom_array( | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/ccd.py", line 88, in get_component_atom_array | |
| ccd_cif = biotite_load_ccd_cif() | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/ccd.py", line 45, in biotite_load_ccd_cif | |
| return pdbx.CIFFile.read(COMPONENTS_FILE) | |
| File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/biotite/structure/io/pdbx/cif.py", line 844, in read | |
| with open(file, "r") as f: | |
| FileNotFoundError: [Errno 2] No such file or directory: '/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/release_data/ccd_cache/components.v20240608.cif' | |
| [Rank 0]7pzb Protenix.get_pairformer_output() missing 1 required positional argument: 'pairformer_stack': | |
| Traceback (most recent call last): | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 260, in infer_predict | |
| prediction, label_dict = runner.predict(data) | |
| File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context | |
| return func(*args, **kwargs) | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 156, in predict | |
| prediction, label_dict, _ = self.model( | |
| File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl | |
| return self._call_impl(*args, **kwargs) | |
| File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl | |
| return forward_call(*args, **kwargs) | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 865, in forward | |
| pred_dict, label_dict, log_dict, time_tracker = self.main_inference_loop( | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 339, in main_inference_loop | |
| pred_dict, log_dict, time_tracker = self._main_inference_loop( | |
| File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 401, in _main_inference_loop | |
| s_inputs, s, z = self.get_pairformer_output( | |
| TypeError: Protenix.get_pairformer_output() missing 1 required positional argument: 'pairformer_stack' | |