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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 11 new columns ({'tested', 'max_log10q', 'null_maxlog10q_std', 'significant', 'null_sig_std', 'null_maxlog10q_p', 'null_sig_p', 'null_sig_mean', 'min_q', 'max_er', 'null_maxlog10q_mean'}) and 9 missing columns ({'value', 'g_global', 'cluster', 'p_value', 'N_total', 'n_cluster', 'q_value', 'enrichment_ratio', 'a_overlap'}).
This happened while the csv dataset builder was generating data using
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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/python3.12/site-packages/datasets/builder.py", line 1890, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 760, in write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2272, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2218, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
seed: int64
attr_type: string
tested: int64
significant: int64
max_er: double
min_q: double
max_log10q: double
null_sig_mean: double
null_sig_std: double
null_sig_p: double
null_maxlog10q_mean: double
null_maxlog10q_std: double
null_maxlog10q_p: double
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1838
to
{'seed': Value('int64'), 'attr_type': Value('string'), 'cluster': Value('int64'), 'value': Value('string'), 'N_total': Value('int64'), 'n_cluster': Value('int64'), 'g_global': Value('int64'), 'a_overlap': Value('int64'), 'p_value': Value('float64'), 'q_value': Value('float64'), 'enrichment_ratio': Value('float64')}
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 1347, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 884, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 947, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1739, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1892, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
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 11 new columns ({'tested', 'max_log10q', 'null_maxlog10q_std', 'significant', 'null_sig_std', 'null_maxlog10q_p', 'null_sig_p', 'null_sig_mean', 'min_q', 'max_er', 'null_maxlog10q_mean'}) and 9 missing columns ({'value', 'g_global', 'cluster', 'p_value', 'N_total', 'n_cluster', 'q_value', 'enrichment_ratio', 'a_overlap'}).
This happened while the csv dataset builder was generating data using
hf://datasets/si3g/GoldenF-data/outputs/runs/single_085_090_human_only_20260306_032339/subset085/reports/validation/fusion_validation_subset085/meta_enrichment_seed_summary.csv (at revision fede8a73e09e0ffdf1fa9e4d54ce84d7bba36217), [/tmp/hf-datasets-cache/medium/datasets/28475703511760-config-parquet-and-info-si3g-GoldenF-data-bd4b641f/hub/datasets--si3g--GoldenF-data/snapshots/fede8a73e09e0ffdf1fa9e4d54ce84d7bba36217/outputs/runs/single_085_090_human_only_20260306_032339/subset085/reports/validation/fusion_validation_subset085/meta_enrichment_results.csv (origin=hf://datasets/si3g/GoldenF-data@fede8a73e09e0ffdf1fa9e4d54ce84d7bba36217/outputs/runs/single_085_090_human_only_20260306_032339/subset085/reports/validation/fusion_validation_subset085/meta_enrichment_results.csv), 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seed int64 | attr_type string | cluster int64 | value string | N_total int64 | n_cluster int64 | g_global int64 | a_overlap int64 | p_value float64 | q_value float64 | enrichment_ratio float64 |
|---|---|---|---|---|---|---|---|---|---|---|
11 | mesh | 0 | Liposomes | 4,298 | 679 | 61 | 51 | 0 | 0 | 5.292209 |
11 | mesh | 0 | Nanoparticles | 4,298 | 679 | 65 | 51 | 0 | 0 | 4.966534 |
11 | mesh | 0 | Hematopoietic Stem Cells | 4,298 | 679 | 102 | 56 | 0 | 0 | 3.475238 |
11 | mesh | 0 | Gene Editing | 4,298 | 679 | 122 | 62 | 0 | 0 | 3.216833 |
11 | mesh | 0 | Tumor Suppressor Protein p53 | 4,298 | 679 | 134 | 57 | 0 | 0 | 2.692568 |
11 | mesh | 0 | Splicing Factor U2AF | 4,298 | 679 | 37 | 26 | 0 | 0 | 4.448036 |
11 | mesh | 0 | CRISPR-Cas Systems | 4,298 | 679 | 150 | 60 | 0 | 0 | 2.531959 |
11 | mesh | 0 | RNA | 4,298 | 679 | 167 | 64 | 0 | 0 | 2.425829 |
11 | mesh | 0 | Diethylhexyl Phthalate | 4,298 | 679 | 29 | 22 | 0 | 0 | 4.801991 |
11 | mesh | 0 | Phthalic Acids | 4,298 | 679 | 29 | 22 | 0 | 0 | 4.801991 |
11 | mesh | 1 | Alleles | 4,298 | 548 | 141 | 44 | 0 | 0.000001 | 2.447481 |
11 | mesh | 1 | Genomics | 4,298 | 548 | 123 | 37 | 0 | 0.000031 | 2.359296 |
11 | mesh | 1 | Myeloid Cells | 4,298 | 548 | 37 | 17 | 0.000001 | 0.000083 | 3.603571 |
11 | mesh | 1 | Polymorphism, Single Nucleotide | 4,298 | 548 | 153 | 41 | 0.000001 | 0.000155 | 2.101737 |
11 | mesh | 1 | Single-Cell Gene Expression Analysis | 4,298 | 548 | 18 | 11 | 0.000002 | 0.000187 | 4.792985 |
11 | mesh | 1 | Albinism, Oculocutaneous | 4,298 | 548 | 98 | 30 | 0.000002 | 0.000208 | 2.400938 |
11 | mesh | 1 | Melanins | 4,298 | 548 | 98 | 30 | 0.000002 | 0.000208 | 2.400938 |
11 | mesh | 1 | Pigmentation | 4,298 | 548 | 98 | 30 | 0.000002 | 0.000208 | 2.400938 |
11 | mesh | 1 | Skin Pigmentation | 4,298 | 548 | 98 | 30 | 0.000002 | 0.000208 | 2.400938 |
11 | mesh | 1 | Cerebral Cortex | 4,298 | 548 | 17 | 10 | 0.000009 | 0.000741 | 4.613568 |
11 | mesh | 2 | Adrenocorticotropic Hormone | 4,298 | 363 | 7 | 7 | 0 | 0.000005 | 11.84022 |
11 | mesh | 2 | Aldosterone | 4,298 | 363 | 7 | 7 | 0 | 0.000005 | 11.84022 |
11 | mesh | 2 | Angiotensin II | 4,298 | 363 | 7 | 7 | 0 | 0.000005 | 11.84022 |
11 | mesh | 2 | Hydrocortisone | 4,298 | 363 | 7 | 7 | 0 | 0.000005 | 11.84022 |
11 | mesh | 2 | MAP Kinase Kinase Kinase 7 | 4,298 | 363 | 7 | 7 | 0 | 0.000005 | 11.84022 |
11 | mesh | 2 | Cyclin A2 | 4,298 | 363 | 9 | 7 | 0.000001 | 0.000098 | 9.20906 |
11 | mesh | 2 | Fluvastatin | 4,298 | 363 | 9 | 7 | 0.000001 | 0.000098 | 9.20906 |
11 | mesh | 2 | Hydroxymethylglutaryl-CoA Reductase Inhibitors | 4,298 | 363 | 9 | 7 | 0.000001 | 0.000098 | 9.20906 |
11 | mesh | 2 | Lovastatin | 4,298 | 363 | 9 | 7 | 0.000001 | 0.000098 | 9.20906 |
11 | mesh | 2 | Simvastatin | 4,298 | 363 | 9 | 7 | 0.000001 | 0.000098 | 9.20906 |
11 | mesh | 3 | Oxygen Consumption | 4,298 | 677 | 12 | 9 | 0.000008 | 0.000681 | 4.761448 |
11 | mesh | 3 | Cardiorespiratory Fitness | 4,298 | 677 | 8 | 7 | 0.000016 | 0.001149 | 5.555022 |
11 | mesh | 3 | Fatty Acids | 4,298 | 677 | 8 | 7 | 0.000016 | 0.001149 | 5.555022 |
11 | mesh | 3 | Oligonucleotides | 4,298 | 677 | 8 | 7 | 0.000016 | 0.001149 | 5.555022 |
11 | mesh | 3 | Pediatric Obesity | 4,298 | 677 | 8 | 7 | 0.000016 | 0.001149 | 5.555022 |
11 | mesh | 3 | Precision Medicine | 4,298 | 677 | 22 | 12 | 0.00003 | 0.00198 | 3.462871 |
11 | mesh | 3 | Adenosine | 4,298 | 677 | 29 | 14 | 0.000039 | 0.002409 | 3.06484 |
11 | mesh | 3 | Adenocarcinoma of Lung | 4,298 | 677 | 9 | 7 | 0.000063 | 0.003577 | 4.937797 |
11 | mesh | 3 | Regulatory Elements, Transcriptional | 4,298 | 677 | 24 | 12 | 0.000092 | 0.004969 | 3.174298 |
11 | mesh | 3 | Tertiary Lymphoid Structures | 4,298 | 677 | 12 | 8 | 0.0001 | 0.005361 | 4.232398 |
11 | mesh | 4 | Receptors, Interferon | 4,298 | 160 | 41 | 23 | 0 | 0 | 15.069207 |
11 | mesh | 4 | Janus Kinases | 4,298 | 160 | 49 | 23 | 0 | 0 | 12.608929 |
11 | mesh | 4 | STAT1 Transcription Factor | 4,298 | 160 | 50 | 23 | 0 | 0 | 12.35675 |
11 | mesh | 4 | Interferons | 4,298 | 160 | 80 | 27 | 0 | 0 | 9.066094 |
11 | mesh | 4 | Antiviral Agents | 4,298 | 160 | 69 | 24 | 0 | 0 | 9.343478 |
11 | mesh | 4 | Interferon Type I | 4,298 | 160 | 119 | 27 | 0 | 0 | 6.094853 |
11 | mesh | 4 | Ligands | 4,298 | 160 | 94 | 24 | 0 | 0 | 6.858511 |
11 | mesh | 4 | Phosphorylation | 4,298 | 160 | 127 | 26 | 0 | 0 | 5.499409 |
11 | mesh | 4 | Signal Transduction | 4,298 | 160 | 497 | 44 | 0 | 0.000003 | 2.378169 |
11 | mesh | 4 | G-Protein-Coupled Receptor Kinase 1 | 4,298 | 160 | 15 | 5 | 0.000149 | 0.007155 | 8.954167 |
11 | mesh | 5 | HSP70 Heat-Shock Proteins | 4,298 | 630 | 18 | 18 | 0 | 0 | 6.822222 |
11 | mesh | 5 | NF-E2-Related Factor 1 | 4,298 | 630 | 18 | 18 | 0 | 0 | 6.822222 |
11 | mesh | 5 | Proteasome Inhibitors | 4,298 | 630 | 18 | 18 | 0 | 0 | 6.822222 |
11 | mesh | 5 | Proteostasis | 4,298 | 630 | 18 | 18 | 0 | 0 | 6.822222 |
11 | mesh | 5 | Proteasome Endopeptidase Complex | 4,298 | 630 | 21 | 18 | 0 | 0 | 5.847619 |
11 | mesh | 5 | Gene Knockout Techniques | 4,298 | 630 | 31 | 18 | 0 | 0.000005 | 3.96129 |
11 | mesh | 5 | Cell Differentiation | 4,298 | 630 | 339 | 86 | 0 | 0.000007 | 1.730711 |
11 | mesh | 5 | A549 Cells | 4,298 | 630 | 39 | 20 | 0 | 0.000011 | 3.498575 |
11 | mesh | 5 | Gene Knockdown Techniques | 4,298 | 630 | 56 | 24 | 0 | 0.000039 | 2.92381 |
11 | mesh | 5 | Adipogenesis | 4,298 | 630 | 20 | 13 | 0 | 0.00005 | 4.434444 |
11 | mesh | 6 | Glycolysis | 4,298 | 632 | 15 | 11 | 0 | 0.000065 | 4.987131 |
11 | mesh | 6 | RNA Interference | 4,298 | 632 | 81 | 28 | 0.000005 | 0.000474 | 2.350836 |
11 | mesh | 6 | Apoptosis Inducing Factor | 4,298 | 632 | 6 | 6 | 0.00001 | 0.00077 | 6.800633 |
11 | mesh | 6 | Electron Transport Complex I | 4,298 | 632 | 6 | 6 | 0.00001 | 0.00077 | 6.800633 |
11 | mesh | 6 | Isocitrate Dehydrogenase | 4,298 | 632 | 6 | 6 | 0.00001 | 0.00077 | 6.800633 |
11 | mesh | 6 | Ketoglutaric Acids | 4,298 | 632 | 6 | 6 | 0.00001 | 0.00077 | 6.800633 |
11 | mesh | 6 | Oxadiazoles | 4,298 | 632 | 6 | 6 | 0.00001 | 0.00077 | 6.800633 |
11 | mesh | 6 | Hematopoiesis | 4,298 | 632 | 33 | 15 | 0.000022 | 0.001484 | 3.091197 |
11 | mesh | 6 | Nonsense Mediated mRNA Decay | 4,298 | 632 | 67 | 23 | 0.000042 | 0.002569 | 2.334546 |
11 | mesh | 6 | Small Molecule Libraries | 4,298 | 632 | 49 | 18 | 0.000107 | 0.005655 | 2.498192 |
11 | mesh | 7 | Male | 4,298 | 259 | 571 | 114 | 0 | 0 | 3.313106 |
11 | mesh | 7 | Female | 4,298 | 259 | 689 | 120 | 0 | 0 | 2.890205 |
11 | mesh | 7 | Adult | 4,298 | 259 | 185 | 57 | 0 | 0 | 5.112929 |
11 | mesh | 7 | Muscle, Skeletal | 4,298 | 259 | 37 | 22 | 0 | 0 | 9.867056 |
11 | mesh | 7 | Middle Aged | 4,298 | 259 | 154 | 42 | 0 | 0 | 4.525799 |
11 | mesh | 7 | Pregnancy | 4,298 | 259 | 73 | 29 | 0 | 0 | 6.592373 |
11 | mesh | 7 | Placenta | 4,298 | 259 | 47 | 21 | 0 | 0 | 7.414606 |
11 | mesh | 7 | Sex Factors | 4,298 | 259 | 16 | 12 | 0 | 0 | 12.445946 |
11 | mesh | 7 | Young Adult | 4,298 | 259 | 48 | 19 | 0 | 0 | 6.568694 |
11 | mesh | 7 | Gestational Age | 4,298 | 259 | 9 | 9 | 0 | 0 | 16.594595 |
11 | mesh | 8 | Antibodies, Antiphospholipid | 4,298 | 107 | 18 | 12 | 0 | 0 | 26.778816 |
11 | mesh | 8 | Anticoagulants | 4,298 | 107 | 18 | 12 | 0 | 0 | 26.778816 |
11 | mesh | 8 | Antiphospholipid Syndrome | 4,298 | 107 | 18 | 12 | 0 | 0 | 26.778816 |
11 | mesh | 8 | Mice, Inbred MRL lpr | 4,298 | 107 | 18 | 12 | 0 | 0 | 26.778816 |
11 | mesh | 8 | Phospholipids | 4,298 | 107 | 18 | 12 | 0 | 0 | 26.778816 |
11 | mesh | 8 | Thromboplastin | 4,298 | 107 | 18 | 12 | 0 | 0 | 26.778816 |
11 | mesh | 8 | Virus Diseases | 4,298 | 107 | 29 | 12 | 0 | 0 | 16.621334 |
11 | mesh | 8 | Immunity, Innate | 4,298 | 107 | 45 | 12 | 0 | 0 | 10.711526 |
11 | mesh | 8 | COVID-19 | 4,298 | 107 | 95 | 14 | 0 | 0.000009 | 5.919528 |
11 | mesh | 8 | Lipopolysaccharides | 4,298 | 107 | 13 | 6 | 0 | 0.000043 | 18.53918 |
11 | mesh | 9 | Aldehyde Dehydrogenase | 4,298 | 243 | 5 | 5 | 0.000001 | 0.000071 | 17.687243 |
11 | mesh | 9 | Bone Neoplasms | 4,298 | 243 | 8 | 6 | 0.000001 | 0.00009 | 13.265432 |
11 | mesh | 9 | Bone and Bones | 4,298 | 243 | 8 | 6 | 0.000001 | 0.00009 | 13.265432 |
11 | mesh | 9 | Clonal Evolution | 4,298 | 243 | 8 | 6 | 0.000001 | 0.00009 | 13.265432 |
11 | mesh | 9 | Gap Junctions | 4,298 | 243 | 8 | 6 | 0.000001 | 0.00009 | 13.265432 |
11 | mesh | 9 | Neoplasm Micrometastasis | 4,298 | 243 | 8 | 6 | 0.000001 | 0.00009 | 13.265432 |
11 | mesh | 9 | Ribosomes | 4,298 | 243 | 39 | 11 | 0.000006 | 0.000536 | 4.98871 |
11 | mesh | 9 | Mice, Knockout | 4,298 | 243 | 67 | 14 | 0.000015 | 0.001136 | 3.695842 |
11 | mesh | 9 | Craniofacial Abnormalities | 4,298 | 243 | 18 | 7 | 0.000032 | 0.002005 | 6.878372 |
11 | mesh | 9 | Ribonucleoproteins | 4,298 | 243 | 9 | 5 | 0.000058 | 0.00345 | 9.826246 |
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