newww

cutlass

@@ -1 +0,0 @@
-Subproject commit f7b19de32c5d1f3cedfc735c2849f12b537522ee

output/ERR/7pzb.txt

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

@@ -1,43 +0,0 @@
-'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

@@ -1,165 +0,0 @@
-[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

@@ -1,40 +0,0 @@
-[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/example_output/predictions/7pzb_need_search_msa_full_data_sample_0.json

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output/example_output/predictions/7pzb_need_search_msa_full_data_sample_1.json

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output/example_output/predictions/7pzb_need_search_msa_full_data_sample_2.json

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output/example_output/predictions/7pzb_need_search_msa_full_data_sample_3.json

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output/example_output/predictions/7pzb_need_search_msa_full_data_sample_4.json

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output/example_output/predictions/7pzb_need_search_msa_seed_101_summary_confidence_sample_0.json

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output/example_output/predictions/7pzb_need_search_msa_seed_101_summary_confidence_sample_1.json

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output/example_output/predictions/7pzb_need_search_msa_seed_101_summary_confidence_sample_3.json

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