UnpicklingError: pickle data was truncated

[alexpBCR]

Hello,

I am getting the following error while trying to predict a single protein:

2025-01-21 16:22:40,352 [/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/infer_data_pipeline.py:209] INFO protenix.data.infer_data_pipeline: Featurizing T1104...
2025-01-21 16:22:50,784 [/home/alexpapadopoulos/.local/lib/python3.10/site-packages/runner/inference.py:240] INFO runner.inference: pickle data was truncated:
Traceback (most recent call last):
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/infer_data_pipeline.py", line 211, in getitem
data, atom_array, _ = self.process_one(
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/infer_data_pipeline.py", line 101, in process_one
sample2feat = SampleDictToFeatures(
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/json_to_feature.py", line 34, in init
self.input_dict = add_entity_atom_array(single_sample_dict)
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/json_parser.py", line 605, in add_entity_atom_array
atom_info = build_polymer(entity_info)
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/json_parser.py", line 364, in build_polymer
chain_array = add_reference_features(chain_array)
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/json_parser.py", line 107, in add_reference_features
ref_info = ccd.get_ccd_ref_info(res_name)
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/ccd.py", line 243, in get_ccd_ref_info
mol = get_component_rdkit_mol(ccd_code)
File "/home/alexpapadopoulos/.local/lib/python3.10/site-packages/protenix/data/ccd.py", line 209, in get_component_rdkit_mol
_ccd_rdkit_mols = pickle.load(f)
_pickle.UnpicklingError: pickle data was truncated

Json file used:

[
{
"sequences": [
{
"proteinChain": {
"sequence": "QLEDSEVEAVAKGLEEMYANGVTEDNFKNYVKNNFAQQEISSVEEELNVNISDSCVANKIKDEFFAMISISAIVKAAQKKAWKELAVTVLRFAKANGLKTNAIIVAGQLALWAVQCG",
"count": 1,
"msa": {
"precomputed_msa_dir": "/media/data/protenix_predictions/casp15/T1104/msa_resmsa_seq_0/0",
"pairing_db": "uniref100"
}
}
}
],
"name": "T1104"
}
]

The Json file was generated with the msa field, using the --use-msa-server.

Anything I'm doing wrong here?

[zhangyuxuann]

@alexpBCR Could you check the integrity of the components.v20240608.cif (md5sum c5bb021a23c63de5f3a79cdb0d4c3921) and components.v20240608.cif.rdkit_mol.pkl (md5sum dc1053d739b68489476c2c424d1e836f) files downloaded? if not, you can delete it and try again

[zhangyuxuann]

@alexpBCR I run your case locally, and it works.

protenix predict --input examples/57.json --out_dir  ./output --seeds 101 --use_msa_server