neww

output/0cb288e2/output.csv

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output/1aaca63d/output.csv

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+"entity_1_id","chain_1_id","mol_1_type","cluster_1_id","entity_2_id","chain_2_id","mol_2_type","cluster_2_id","cluster_id","pdb_id","assembly_id","release_date","num_tokens","num_prot_chains","resolution","type","mol_type_group","sub_mol_1_type","sub_mol_2_type","eval_type"
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output/20250208_090556_01481199.json

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+oid sha256:e34280fe1c1cc68c293c61d242bfbe84ea82f3ca6e3a33778767606b6d0f6dd8
+size 745

output/6bf94bd0/output.csv

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+"entity_1_id","chain_1_id","mol_1_type","cluster_1_id","entity_2_id","chain_2_id","mol_2_type","cluster_2_id","cluster_id","pdb_id","assembly_id","release_date","num_tokens","num_prot_chains","resolution","type","mol_type_group","sub_mol_1_type","sub_mol_2_type","eval_type"
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output/ERR/7pzb.txt

@@ -0,0 +1,40 @@
+[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'

output/ERR/7pzb_need_search_msa.txt

@@ -0,0 +1,43 @@
+'msa':
+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 114, in process_one
+    InferenceMSAFeaturizer.make_msa_feature(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/msa_featurizer.py", line 1144, in make_msa_feature
+    msa_feats = InferenceMSAFeaturizer.get_inference_prot_msa_features_for_assembly(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/msa_featurizer.py", line 1047, in get_inference_prot_msa_features_for_assembly
+    msa_info = bioassembly[int(entity_id_list[0]) - 1][PROT_TYPE_NAME]["msa"]
+KeyError: 'msa'
+'msa':
+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 114, in process_one
+    InferenceMSAFeaturizer.make_msa_feature(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/msa_featurizer.py", line 1144, in make_msa_feature
+    msa_feats = InferenceMSAFeaturizer.get_inference_prot_msa_features_for_assembly(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/msa_featurizer.py", line 1047, in get_inference_prot_msa_features_for_assembly
+    msa_info = bioassembly[int(entity_id_list[0]) - 1][PROT_TYPE_NAME]["msa"]
+KeyError: 'msa'
+[Rank 0]7pzb_need_search_msa 'watermark':
+Traceback (most recent call last):
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 338, 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 158, 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 1041, 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 521, in main_inference_loop
+    "watermark": _cat(pred_dicts, "watermark")
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 508, in _cat
+    return torch.cat([x[key] for x in dict_list], dim=0)
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 508, in <listcomp>
+    return torch.cat([x[key] for x in dict_list], dim=0)
+KeyError: 'watermark'

output/ERR/7r6r.txt

@@ -0,0 +1,165 @@
+[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]7r6r 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'
+[Rank 0]7r6r [Errno 28] No space left on device: '/n/home09/zaixizhang/.cache/torch_extensions/py310_cu121/evoformer_attn/lock':
+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 866, 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(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 202, in get_pairformer_output
+    z = self.msa_module(
+  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/modules/pairformer.py", line 732, in forward
+    msa_sample, z = checkpoint_blocks(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/utils/checkpointing.py", line 85, in checkpoint_blocks
+    return exec(blocks, args)
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/utils/checkpointing.py", line 72, in exec
+    a = wrap(block(*a))
+  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/modules/pairformer.py", line 517, in forward
+    _, z = self.pair_stack(
+  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/modules/pairformer.py", line 132, in forward
+    z += self.tri_att_start(
+  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/openfold_local/model/triangular_attention.py", line 129, in forward
+    x = self._chunk(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/model/triangular_attention.py", line 74, in _chunk
+    return chunk_layer(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/utils/chunk_utils.py", line 285, in chunk_layer
+    output_chunk = layer(**chunks)
+  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/openfold_local/model/primitives.py", line 560, in forward
+    o = _deepspeed_evo_attn(q, k, v, biases)
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/model/primitives.py", line 730, in _deepspeed_evo_attn
+    o = DS4Sci_EvoformerAttention(q, k, v, biases)
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/deepspeed4science/evoformer_attn.py", line 106, in DS4Sci_EvoformerAttention
+    return EvoformerFusedAttention.apply(Q, K, V, biases[0], biases[1])
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/autograd/function.py", line 598, in apply
+    return super().apply(*args, **kwargs)  # type: ignore[misc]
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/deepspeed4science/evoformer_attn.py", line 71, in forward
+    o, lse = _attention(q, k, v, bias1_, bias2_)
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/deepspeed4science/evoformer_attn.py", line 24, in _attention
+    kernel_ = EvoformerAttnBuilder().load()
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/op_builder/builder.py", line 508, in load
+    return self.jit_load(verbose)
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/op_builder/builder.py", line 555, in jit_load
+    op_module = load(name=self.name,
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1309, in load
+    return _jit_compile(
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1696, in _jit_compile
+    if baton.try_acquire():
+  File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/file_baton.py", line 29, in try_acquire
+    self.fd = os.open(self.lock_file_path, os.O_CREAT | os.O_EXCL)
+OSError: [Errno 28] No space left on device: '/n/home09/zaixizhang/.cache/torch_extensions/py310_cu121/evoformer_attn/lock'
+[Rank 0]7r6r 'profile':
+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 866, 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 523, in _main_inference_loop
+    s_inputs_clean, s_clean, z_clean = self.get_pairformer_output(
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 159, in get_pairformer_output
+    s_inputs = self.input_embedder(
+  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/modules/embedders.py", line 81, in forward
+    + [
+  File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/modules/embedders.py", line 82, in <listcomp>
+    input_feature_dict[name].reshape(*batch_shape, d)
+KeyError: 'profile'
+[Rank 0]7r6r too many values to unpack (expected 3):
+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 867, 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(
+ValueError: too many values to unpack (expected 3)

output/ERR/7wux.txt

@@ -0,0 +1,40 @@
+[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]7wux 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'

output/ba2750f6/output.csv

@@ -0,0 +1,7 @@
+"entity_1_id","chain_1_id","mol_1_type","cluster_1_id","entity_2_id","chain_2_id","mol_2_type","cluster_2_id","cluster_id","pdb_id","assembly_id","release_date","num_tokens","num_prot_chains","resolution","type","mol_type_group","sub_mol_1_type","sub_mol_2_type","eval_type"
+"1","A","prot","NotInClusterTxt","","","","","NotInClusterTxt","7r6r","","9999-12-31",245,1,-1.0,"chain","intra_prot","prot","","intra_prot"
+"2","B","nuc","TTTCGGTGGCTGTCAAGCGGG","","","","","TTTCGGTGGCTGTCAAGCGGG","7r6r","","9999-12-31",245,1,-1.0,"chain","intra_nuc","dna","","intra_dna"
+"3","C","nuc","CCCGCTTGACAGCCACCGAAA","","","","","CCCGCTTGACAGCCACCGAAA","7r6r","","9999-12-31",245,1,-1.0,"chain","intra_nuc","dna","","intra_dna"
+"1","A","prot","NotInClusterTxt","2","B","nuc","TTTCGGTGGCTGTCAAGCGGG","NotInClusterTxt:TTTCGGTGGCTGTCAAGCGGG","7r6r","","9999-12-31",245,1,-1.0,"interface","nuc_prot","prot","dna","dna_prot"
+"1","A","prot","NotInClusterTxt","3","C","nuc","CCCGCTTGACAGCCACCGAAA","CCCGCTTGACAGCCACCGAAA:NotInClusterTxt","7r6r","","9999-12-31",245,1,-1.0,"interface","nuc_prot","prot","dna","dna_prot"
+"2","B","nuc","TTTCGGTGGCTGTCAAGCGGG","3","C","nuc","CCCGCTTGACAGCCACCGAAA","CCCGCTTGACAGCCACCGAAA:TTTCGGTGGCTGTCAAGCGGG","7r6r","","9999-12-31",245,1,-1.0,"interface","nuc_nuc","dna","dna","nuc_nuc"

output/c71cae44/output.csv

@@ -0,0 +1,23 @@
+"entity_1_id","chain_1_id","mol_1_type","cluster_1_id","entity_2_id","chain_2_id","mol_2_type","cluster_2_id","cluster_id","pdb_id","assembly_id","release_date","num_tokens","num_prot_chains","resolution","type","mol_type_group","sub_mol_1_type","sub_mol_2_type","eval_type"
+"1","A","prot","NotInClusterTxt","","","","","NotInClusterTxt","7pzb","","9999-12-31",600,2,-1.0,"chain","intra_prot","prot","","intra_prot"
+"1","B","prot","NotInClusterTxt","","","","","NotInClusterTxt","7pzb","","9999-12-31",600,2,-1.0,"chain","intra_prot","prot","","intra_prot"
+"2","C","nuc","CTAGGTAACATTACTCGCG","","","","","CTAGGTAACATTACTCGCG","7pzb","","9999-12-31",600,2,-1.0,"chain","intra_nuc","dna","","intra_dna"
+"2","D","nuc","CTAGGTAACATTACTCGCG","","","","","CTAGGTAACATTACTCGCG","7pzb","","9999-12-31",600,2,-1.0,"chain","intra_nuc","dna","","intra_dna"
+"3","E","nuc","GCGAGTAATGTTAC","","","","","GCGAGTAATGTTAC","7pzb","","9999-12-31",600,2,-1.0,"chain","intra_nuc","dna","","intra_dna"
+"3","F","nuc","GCGAGTAATGTTAC","","","","","GCGAGTAATGTTAC","7pzb","","9999-12-31",600,2,-1.0,"chain","intra_nuc","dna","","intra_dna"
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