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[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'
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