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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 4 new columns ({'sequence', 'gene_length', 'strand', 'gene'}) and 1 missing columns ({'\tUnnamed: 0\tvariant\tchr\tpos\tref\talt\teffect_allele\tother_allele\tgene\tgene_symbol\teffect_size\tlog2_fold_change\tp_nominal_nlog10\tfdr_nlog10\tfdr_method\tpower\tVariantID_h19\tvariant_sequence'}).
This happened while the csv dataset builder was generating data using
hf://datasets/deBoerLab/Martyn_VariantEffects_GAME/evaluator_data/gene_reference_sequences.csv (at revision f6b670c805eb76d7a768aa60ad3e290386beae8d), ['hf://datasets/deBoerLab/Martyn_VariantEffects_GAME@f6b670c805eb76d7a768aa60ad3e290386beae8d/evaluator_data/Jurkat/variant_sequences.csv', 'hf://datasets/deBoerLab/Martyn_VariantEffects_GAME@f6b670c805eb76d7a768aa60ad3e290386beae8d/evaluator_data/THP1/variant_sequences.csv', 'hf://datasets/deBoerLab/Martyn_VariantEffects_GAME@f6b670c805eb76d7a768aa60ad3e290386beae8d/evaluator_data/gene_reference_sequences.csv']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1837, in _prepare_split_single
writer.write_table(table)
~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2369, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2297, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
gene: string
gene_length: int64
strand: string
sequence: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 732
to
{'\tUnnamed: 0\tvariant\tchr\tpos\tref\talt\teffect_allele\tother_allele\tgene\tgene_symbol\teffect_size\tlog2_fold_change\tp_nominal_nlog10\tfdr_nlog10\tfdr_method\tpower\tVariantID_h19\tvariant_sequence': Value('string')}
because column names don't match
During handling of the above exception, another exception occurred:
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 1683, 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 1839, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
...<4 lines>...
)
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 4 new columns ({'sequence', 'gene_length', 'strand', 'gene'}) and 1 missing columns ({'\tUnnamed: 0\tvariant\tchr\tpos\tref\talt\teffect_allele\tother_allele\tgene\tgene_symbol\teffect_size\tlog2_fold_change\tp_nominal_nlog10\tfdr_nlog10\tfdr_method\tpower\tVariantID_h19\tvariant_sequence'}).
This happened while the csv dataset builder was generating data using
hf://datasets/deBoerLab/Martyn_VariantEffects_GAME/evaluator_data/gene_reference_sequences.csv (at revision f6b670c805eb76d7a768aa60ad3e290386beae8d), ['hf://datasets/deBoerLab/Martyn_VariantEffects_GAME@f6b670c805eb76d7a768aa60ad3e290386beae8d/evaluator_data/Jurkat/variant_sequences.csv', 'hf://datasets/deBoerLab/Martyn_VariantEffects_GAME@f6b670c805eb76d7a768aa60ad3e290386beae8d/evaluator_data/THP1/variant_sequences.csv', 'hf://datasets/deBoerLab/Martyn_VariantEffects_GAME@f6b670c805eb76d7a768aa60ad3e290386beae8d/evaluator_data/gene_reference_sequences.csv']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Unnamed: 0 variant chr pos ref alt effect_allele other_allele gene gene_symbol effect_size log2_fold_change p_nominal_nlog10 fdr_nlog10 fdr_method power VariantID_h19 variant_sequence string |
|---|
"0\t0\tNC_000010.11:79347410::AACGGAGC\tchr10\t79347410\t\tAACGGAGC\tAACGGAGC\t\tENSG00000108179\tPP(...TRUNCATED) |
"1\t1\tNC_000010.11:79347410::AAGATGGC\tchr10\t79347410\t\tAAGATGGC\tAAGATGGC\t\tENSG00000108179\tPP(...TRUNCATED) |
"2\t2\tNC_000010.11:79347410::AAGTAGGC\tchr10\t79347410\t\tAAGTAGGC\tAAGTAGGC\t\tENSG00000108179\tPP(...TRUNCATED) |
"3\t3\tNC_000010.11:79347410::ACAGTCAT\tchr10\t79347410\t\tACAGTCAT\tACAGTCAT\t\tENSG00000108179\tPP(...TRUNCATED) |
"4\t4\tNC_000010.11:79347410::ACCATCCA\tchr10\t79347410\t\tACCATCCA\tACCATCCA\t\tENSG00000108179\tPP(...TRUNCATED) |
"5\t5\tNC_000010.11:79347410::ACCATGGA\tchr10\t79347410\t\tACCATGGA\tACCATGGA\t\tENSG00000108179\tPP(...TRUNCATED) |
"6\t6\tNC_000010.11:79347409:G:GACCGCTAG\tchr10\t79347409\tG\tGACCGCTAG\tGACCGCTAG\tG\tENSG000001081(...TRUNCATED) |
"7\t7\tNC_000010.11:79347409:G:GACCGGAAG\tchr10\t79347409\tG\tGACCGGAAG\tGACCGGAAG\tG\tENSG000001081(...TRUNCATED) |
"8\t8\tNC_000010.11:79347410::ACTTAAGA\tchr10\t79347410\t\tACTTAAGA\tACTTAAGA\t\tENSG00000108179\tPP(...TRUNCATED) |
"9\t9\tNC_000010.11:79347410::AGAGAGCC\tchr10\t79347410\t\tAGAGAGCC\tAGAGAGCC\t\tENSG00000108179\tPP(...TRUNCATED) |
End of preview.
YAML Metadata Warning:empty or missing yaml metadata in repo card
Check out the documentation for more information.
Module Version: martyn_variant_effects_20260610-163836_EDT
GAME Schema Version: v 1.0
Github Link: https://github.com/de-Boer-Lab/GAME-Martyn-variant-effects-evaluator
Additional information can be found on GitHub: Genomic API for Model Evaluation
Original publication can be found here: Martyn et al., 2025
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