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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1531, in _prepare_split_single
for key, record in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 127, in _generate_examples
for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
for filename, f in tar_iterator:
^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
for x in self.generator(*self.args):
~~~~~~~~~~~~~~^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1405, in _iter_from_urlpath
with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 982, in xopen
file_obj = fs.open(paths[0], mode)
File "<string>", line 3, in open
File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
return self._mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
return self._execute_mock_call(*args, **kwargs)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
result = effect(*args, **kwargs)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
~~~^^^^^^^^
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1393, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1571, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
fasta unknown | __key__ string | __url__ string |
|---|---|---|
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83... | aa_seq/POLG_DEN26_Suphatrakul_2023 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/HCP_LAMBD_Tsuboyama_2023_2L6Q | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/RD23A_HUMAN_Tsuboyama_2023_1IFY | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/DLG4_RAT_McLaughlin_2012 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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7... | aa_seq/RAF1_HUMAN_Zinkus-Boltz_2019 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/SPA_STAAU_Tsuboyama_2023_1LP1 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/SPG1_STRSG_Olson_2014 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/IF1_ECOLI_Kelsic_2016 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/SDA_BACSU_Tsuboyama_2023_1PV0 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/UBE4B_MOUSE_Starita_2013 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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73... | aa_seq/A4D664_9INFA_Soh_2019 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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7... | aa_seq/CAR11_HUMAN_Meitlis_2020_lof | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/DNJA1_HUMAN_Tsuboyama_2023_2LO1 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/CASP3_HUMAN_Roychowdhury_2020 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/HECD1_HUMAN_Tsuboyama_2023_3DKM | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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86,... | aa_seq/SPIKE_SARS2_Starr_2020_expression | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/CASP7_HUMAN_Roychowdhury_2020 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/ILF3_HUMAN_Tsuboyama_2023_2L33 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/ENVZ_ECOLI_Ghose_2023 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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8... | aa_seq/F7YBW8_MESOW_Aakre_2015 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/SC6A4_HUMAN_Young_2021 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/NUSA_ECOLI_Tsuboyama_2023_1WCL | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/VKOR1_HUMAN_Chiasson_2020_abundance | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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7... | aa_seq/POLG_CXB3N_Mattenberger_2021 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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8... | aa_seq/Q8WTC7_9CNID_Somermeyer_2022 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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8... | aa_seq/I6TAH8_I68A0_Doud_2015 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/POLG_PESV_Tsuboyama_2023_2MXD | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/SRC_HUMAN_Ahler_2019 | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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... | aa_seq/PITX2_HUMAN_Tsuboyama_2023_2L7M | hf://datasets/AI4Protein/VenusREM-Harness@38d8185882d23dbda9f266b804f81410c67d0d6c/ProteinGym/aa_seq.tar.gz |
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End of preview.
VenusREM2 data
Private archives for rem2 download. Layout is rem2 --base_dir
(aa_seq/, substitutions/, pdbs/, aa_seq_aln_a2m_af2cf/).
ProteinGym default MSA is the paper ColabFold set (aa_seq_aln_a2m_af2cf.tar.gz).
Assay lists match the Overleaf evaluation set: 1,211 assays.
| Folder | Assays | Unique WT | Notes |
|---|---|---|---|
ProteinGym/ |
217 | 187 (186 UniProt) | Official substitution DMS. 217 files per folder, same IDs as the paper panel. |
VenusMutHub/ |
905 | 527 | Same 905 assays as the paper macro-average. Duplicate-WT PDBs are assay-named copies or symlinks. |
VenusViroHub/ |
89 | 52 | Paper set after dropping SARS2_XBB15_RBD_Taylor. 616,690 evaluated substitutions (XnX kept in CSVs, excluded from metrics). Zero assay overlap with ProteinGym. |
VenusViroHub phenotype counts (paper Table): immune escape 21 / 148,468; cell entry 18 / 189,048; binding 17 / 90,245; expression 15 / 58,120; fitness 15 / 114,287; stability 2 / 11,187; activity 1 / 5,335.
Academic / non-profit use is free. Commercial or fee-for-service use requires a license: contact tanyang.august@sjtu.edu.
Do not git clone this repo. Download the .tar.gz files and extract.
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