Datasets:

---

VatsalPatel18

/

Case-Study-HNSCC-ML-Copilot-Agent

like 0

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 23037 new columns ({'MYNN', 'LINC00367', 'GRPEL1', 'EYS', 'LINC00668', 'CNGB3', 'TMEM75', 'ADAMTS1', 'SLC39A2', 'GATA5', 'MIR6069', 'TGFA-IT1', 'GBF1', 'PRG4', 'CD40LG', 'SSX2B', 'CHST5', 'APH1A', 'DNAJB11', 'TMEM14B', 'RALGDS', 'FGFRL1', 'CYP2A7', 'MYT1', 'CD69', 'SNAP29', 'LRRC27', 'STMN1', 'RNF165', 'HGC6.3', 'FNDC5', 'KLRC3', 'CALHM3', 'RAD1', 'SUSD2', 'GOPC', 'GPC3', 'PRC1', 'LZTS1-AS1', 'DMRTB1', 'SNRNP200', 'OR1N1', 'SGCG', 'UBQLN1', 'G6PC2', 'SNORD113-1', 'RASA3', 'NCOA7', 'PRDM7', 'MIR3202-1', 'MED24', 'YBX1', 'RPL15', 'CSTB', 'LOC102723376', 'PHACTR2-AS1', 'TPT1-AS1', 'LOC100288069', 'KCMF1', 'FUT9', 'ZNF891', 'PRAF2', 'YWHAE', 'ZAR1L', 'CACNG5', 'MRPS33', 'TRIM51', 'UTS2R', 'LOC643711', 'COX7A2L', 'FMR1', 'SLC22A16', 'CCDC74A', 'SLC9A9', 'JAZF1', 'KRTAP10-1', 'SCARNA7', 'BRWD1-IT2', 'LINC00992', 'BCL2', 'HSFX1', 'ZNF358', 'SNORD115-31', 'HOXD13', 'SCMH1', 'LPIN1', 'MB21D1', 'VKORC1L1', 'MIRLET7C', 'TAS2R14', 'GABPA', 'OPN3', 'ZDHHC24', 'SEC14L3', 'NAA20', 'TXLNA', 'MIR124-2', 'SPOPL', 'MIR662', 'ADAM18', 'CCDC129', 'TPRX1', 'CASP9', 'CPT1C', 'DZIP3', 'MIR3179-3', 'FGF19', 'CASC15', 'SCGB1D2', 'SPRY3', 'CYP4F62P', 'MIR204', 'RAB38', 'MIR4686', 'LINC00442', 'MTMR7', 'MIR661', 'PPEF1', 'NF2', 'SPAST', 'KRIT1', 'LAYN', 'SNORD115-45', 'HERC2P9', 'ZNF593', 'AKAP10', 'NINL', 'TNFSF8', 'POMT2', 'RBM24', 'HCST', 'OR6C1', 'RP9P', 'RIPK1', 'COBLL1', 'SNORA40', 'NEIL2', 'SNORD116-4', 'SPINT2', 'MTSS1', 'PRKX-AS1', 'ULBP3', 'KATNBL1P6', 'LINC00347', 'ERCC4', 'MIR4479', 'APCS', 'LINC01001', 'MIR45
...
, 'SMC5-AS1', 'HTATSF1', 'RAB2B', 'PRDM9', 'CSRP1', 'FOXI3', 'ABCC2', 'CERS5', 'SFXN1', 'SLC5A11', 'LINC01134', 'CLN6', 'ARMC8', 'PKHD1', 'STARD5', 'ARHGAP44', 'MFF', 'IGDCC3', 'NEK4', 'AR', 'IL16', 'SNORD31', 'SENP8', 'CNGB1', 'CTF1', 'RBM48', 'IFT57', 'OR4X2', 'LSM4', 'OR9A4', 'SNORD114-10', 'STK32B', 'KLC2', 'MIR4509-2', 'PRR7', 'GABRB3', 'DNAJB13', 'NDUFS5', 'FDX1', 'DVL3', 'TANC1', 'GDNF-AS1', 'CCKAR', 'MIR4460', 'DNAJC25-GNG10', 'CLUAP1', 'PINK1', 'SLC8A3', 'STK32C', 'LOC400655', 'IQCE', 'RPL19P12', 'AP3S1', 'AFG3L2', 'CHIAP2', 'ZNF91', 'PSMD2', 'ANKRD20A19P', 'ADD1', 'CCDC125', 'CEND1', 'TRIM73', 'WBSCR28', 'MIR3121', 'GTPBP8', 'SLC46A1', 'NUB1', 'CD46', 'MYO1E', 'WNT3A', 'GOLGA6L10', 'OR2M7', 'MEFV', 'FAM131C', 'PLGLA', 'CTAGE1', 'ZNF783', 'FOXRED2', 'CEP170', 'SNORA51', 'AZGP1', 'XKR9', 'MIR548AJ2', 'GOLGA6L22', 'PAN3-AS1', 'PHTF2', 'MIR4651', 'ENKUR', 'SPACA7', 'SDHAP1', 'CYP4Z1', 'NCL', 'PCNP', 'SNX1', 'CWF19L2', 'TSNAXIP1', 'LOC148696', 'MIR136', 'IDI2', 'LINC01011', 'RAP1A', 'PCDHA13', 'LAMTOR1', 'GLUD1P3', 'ZDHHC21', 'FAM25C', 'BIRC8', 'OR1S1', 'OR13C2', 'SYNPO', 'ANGPTL2', 'ADAT2', 'TREH', 'MIR1182', 'ZBTB8B', 'ZFAND2A', 'MIR3978', 'PARG', 'MIR6742', 'LOC729609', 'SETDB2', 'LINC00921', 'MCIDAS', 'SPATA31E1', 'TNFRSF1A', 'CYP24A1', 'OTUD3', 'TRIP11', 'MIR500B', 'MIR144', 'CD99P1', 'SPACA6P-AS', 'ADAM20', 'PROSER2', 'FBXL17', 'ASCC2', 'PAX2', 'ARPC4', 'POTED', 'OR2L13', 'MTFR1', 'GPR183', 'WFDC8', 'RPS6KA2', 'UBAC2-AS1', 'SLC35G5', 'KIF21A', 'MIR4734', 'SRGAP2D'}) and 3 missing columns ({'Overall Survival Status', 'Unnamed: 0', 'Overall Survival (Months)'}).

This happened while the csv dataset builder was generating data using

hf://datasets/VatsalPatel18/Case-Study-HNSCC-ML-Copilot-Agent/hnscc_data/common_genes.23037.sCNV.TCGA.hpvN.scaled.csv (at revision b8311f15ebaabbb33f7f51693118e17f72176d62)

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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1871, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 623, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2293, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2241, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              PatientID: string
              A1BG: double
              A1BG-AS1: double
              A1CF: double
              A2M: double
              A2M-AS1: double
              A2ML1: double
              A2MP1: double
              A3GALT2: double
              A4GALT: double
              A4GNT: double
              AA06: double
              AAAS: double
              AACS: double
              AACSP1: double
              AADAC: double
              AADACL2: double
              AADACL2-AS1: double
              AADACL3: double
              AADACL4: double
              AADACP1: double
              AADAT: double
              AAED1: double
              AAGAB: double
              AAK1: double
              AAMDC: double
              AAMP: double
              AANAT: double
              AAR2: double
              AARD: double
              AARS: double
              AARS2: double
              AARSD1: double
              AASDH: double
              AASDHPPT: double
              AASS: double
              AATBC: double
              AATF: double
              AATK: double
              AATK-AS1: double
              ABAT: double
              ABCA1: double
              ABCA10: double
              ABCA11P: double
              ABCA12: double
              ABCA13: double
              ABCA17P: double
              ABCA2: double
              ABCA3: double
              ABCA4: double
              ABCA5: double
              ABCA6: double
              ABCA7: double
              ABCA8: double
              ABCA9: double
              ABCB1: double
              ABCB10: double
              ABCB11: double
              ABCB4: double
              ABCB5: double
              ABCB6: double
              ABCB7: double
              ABCB8: double
              ABCB9: double
              ABCC1: double
              ABCC10: double
              ABCC11: double
              ABCC12: double
              ABCC13: double
              ABCC2: double
              ABCC3: double
              ABCC4: double
              ABCC5: double
              ABCC5-AS1: double
              ABCC6: double
              ABCC6P1: double
              ABCC6P2: double
              ABCC8: double
              ABCC9: double
              ABCD1: double
              ABCD2: double
              ABCD3: double
              ABCD4: double
              ABCE1: double
              ABCF1: double
              ABCF2: double
              ABCF3: double
              ABCG1: double
              ABCG2: double
              ABCG4: double
              ABCG5: double
              ABCG8: double
              ABHD1: double
              ABHD10: double
              ABHD11: double
              ABHD12: double
              ABHD12B: double
              ABHD13: double
              ABHD14A: double
              ABHD14A-ACY1: double
              ABHD14B: double
              ABHD15: double
              ABHD16A: double
              ...
              le
              ZNF845: double
              ZNF846: double
              ZNF847P: double
              ZNF85: double
              ZNF850: double
              ZNF852: double
              ZNF853: double
              ZNF860: double
              ZNF862: double
              ZNF865: double
              ZNF876P: double
              ZNF878: double
              ZNF879: double
              ZNF880: double
              ZNF883: double
              ZNF890P: double
              ZNF891: double
              ZNF90: double
              ZNF91: double
              ZNF92: double
              ZNF93: double
              ZNF98: double
              ZNF99: double
              ZNFX1: double
              ZNHIT1: double
              ZNHIT2: double
              ZNHIT3: double
              ZNHIT6: double
              ZNRD1: double
              ZNRF1: double
              ZNRF2: double
              ZNRF2P1: double
              ZNRF2P2: double
              ZNRF3: double
              ZNRF3-AS1: double
              ZNRF4: double
              ZP1: double
              ZP2: double
              ZP3: double
              ZP4: double
              ZPBP: double
              ZPBP2: double
              ZPLD1: double
              ZPR1: double
              ZRANB1: double
              ZRANB2: double
              ZRANB2-AS1: double
              ZRANB2-AS2: double
              ZRANB3: double
              ZRSR2: double
              ZSCAN1: double
              ZSCAN10: double
              ZSCAN12: double
              ZSCAN12P1: double
              ZSCAN16: double
              ZSCAN16-AS1: double
              ZSCAN18: double
              ZSCAN2: double
              ZSCAN20: double
              ZSCAN21: double
              ZSCAN22: double
              ZSCAN23: double
              ZSCAN25: double
              ZSCAN26: double
              ZSCAN29: double
              ZSCAN30: double
              ZSCAN31: double
              ZSCAN32: double
              ZSCAN4: double
              ZSCAN5A: double
              ZSCAN5B: double
              ZSCAN9: double
              ZSWIM1: double
              ZSWIM2: double
              ZSWIM3: double
              ZSWIM4: double
              ZSWIM5: double
              ZSWIM6: double
              ZSWIM7: double
              ZSWIM8: double
              ZSWIM8-AS1: double
              ZUFSP: double
              ZW10: double
              ZWILCH: double
              ZWINT: double
              ZXDA: double
              ZXDB: double
              ZXDC: double
              ZYG11A: double
              ZYG11B: double
              ZYX: double
              ZZEF1: double
              ZZZ3: double
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 2601760
              to
              {'Unnamed: 0': Value(dtype='int64', id=None), 'PatientID': Value(dtype='string', id=None), 'Overall Survival Status': Value(dtype='float64', id=None), 'Overall Survival (Months)': Value(dtype='float64', id=None)}
              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 1438, 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 1050, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 925, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1001, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1742, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1873, 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 23037 new columns ({'MYNN', 'LINC00367', 'GRPEL1', 'EYS', 'LINC00668', 'CNGB3', 'TMEM75', 'ADAMTS1', 'SLC39A2', 'GATA5', 'MIR6069', 'TGFA-IT1', 'GBF1', 'PRG4', 'CD40LG', 'SSX2B', 'CHST5', 'APH1A', 'DNAJB11', 'TMEM14B', 'RALGDS', 'FGFRL1', 'CYP2A7', 'MYT1', 'CD69', 'SNAP29', 'LRRC27', 'STMN1', 'RNF165', 'HGC6.3', 'FNDC5', 'KLRC3', 'CALHM3', 'RAD1', 'SUSD2', 'GOPC', 'GPC3', 'PRC1', 'LZTS1-AS1', 'DMRTB1', 'SNRNP200', 'OR1N1', 'SGCG', 'UBQLN1', 'G6PC2', 'SNORD113-1', 'RASA3', 'NCOA7', 'PRDM7', 'MIR3202-1', 'MED24', 'YBX1', 'RPL15', 'CSTB', 'LOC102723376', 'PHACTR2-AS1', 'TPT1-AS1', 'LOC100288069', 'KCMF1', 'FUT9', 'ZNF891', 'PRAF2', 'YWHAE', 'ZAR1L', 'CACNG5', 'MRPS33', 'TRIM51', 'UTS2R', 'LOC643711', 'COX7A2L', 'FMR1', 'SLC22A16', 'CCDC74A', 'SLC9A9', 'JAZF1', 'KRTAP10-1', 'SCARNA7', 'BRWD1-IT2', 'LINC00992', 'BCL2', 'HSFX1', 'ZNF358', 'SNORD115-31', 'HOXD13', 'SCMH1', 'LPIN1', 'MB21D1', 'VKORC1L1', 'MIRLET7C', 'TAS2R14', 'GABPA', 'OPN3', 'ZDHHC24', 'SEC14L3', 'NAA20', 'TXLNA', 'MIR124-2', 'SPOPL', 'MIR662', 'ADAM18', 'CCDC129', 'TPRX1', 'CASP9', 'CPT1C', 'DZIP3', 'MIR3179-3', 'FGF19', 'CASC15', 'SCGB1D2', 'SPRY3', 'CYP4F62P', 'MIR204', 'RAB38', 'MIR4686', 'LINC00442', 'MTMR7', 'MIR661', 'PPEF1', 'NF2', 'SPAST', 'KRIT1', 'LAYN', 'SNORD115-45', 'HERC2P9', 'ZNF593', 'AKAP10', 'NINL', 'TNFSF8', 'POMT2', 'RBM24', 'HCST', 'OR6C1', 'RP9P', 'RIPK1', 'COBLL1', 'SNORA40', 'NEIL2', 'SNORD116-4', 'SPINT2', 'MTSS1', 'PRKX-AS1', 'ULBP3', 'KATNBL1P6', 'LINC00347', 'ERCC4', 'MIR4479', 'APCS', 'LINC01001', 'MIR45
              ...
              , 'SMC5-AS1', 'HTATSF1', 'RAB2B', 'PRDM9', 'CSRP1', 'FOXI3', 'ABCC2', 'CERS5', 'SFXN1', 'SLC5A11', 'LINC01134', 'CLN6', 'ARMC8', 'PKHD1', 'STARD5', 'ARHGAP44', 'MFF', 'IGDCC3', 'NEK4', 'AR', 'IL16', 'SNORD31', 'SENP8', 'CNGB1', 'CTF1', 'RBM48', 'IFT57', 'OR4X2', 'LSM4', 'OR9A4', 'SNORD114-10', 'STK32B', 'KLC2', 'MIR4509-2', 'PRR7', 'GABRB3', 'DNAJB13', 'NDUFS5', 'FDX1', 'DVL3', 'TANC1', 'GDNF-AS1', 'CCKAR', 'MIR4460', 'DNAJC25-GNG10', 'CLUAP1', 'PINK1', 'SLC8A3', 'STK32C', 'LOC400655', 'IQCE', 'RPL19P12', 'AP3S1', 'AFG3L2', 'CHIAP2', 'ZNF91', 'PSMD2', 'ANKRD20A19P', 'ADD1', 'CCDC125', 'CEND1', 'TRIM73', 'WBSCR28', 'MIR3121', 'GTPBP8', 'SLC46A1', 'NUB1', 'CD46', 'MYO1E', 'WNT3A', 'GOLGA6L10', 'OR2M7', 'MEFV', 'FAM131C', 'PLGLA', 'CTAGE1', 'ZNF783', 'FOXRED2', 'CEP170', 'SNORA51', 'AZGP1', 'XKR9', 'MIR548AJ2', 'GOLGA6L22', 'PAN3-AS1', 'PHTF2', 'MIR4651', 'ENKUR', 'SPACA7', 'SDHAP1', 'CYP4Z1', 'NCL', 'PCNP', 'SNX1', 'CWF19L2', 'TSNAXIP1', 'LOC148696', 'MIR136', 'IDI2', 'LINC01011', 'RAP1A', 'PCDHA13', 'LAMTOR1', 'GLUD1P3', 'ZDHHC21', 'FAM25C', 'BIRC8', 'OR1S1', 'OR13C2', 'SYNPO', 'ANGPTL2', 'ADAT2', 'TREH', 'MIR1182', 'ZBTB8B', 'ZFAND2A', 'MIR3978', 'PARG', 'MIR6742', 'LOC729609', 'SETDB2', 'LINC00921', 'MCIDAS', 'SPATA31E1', 'TNFRSF1A', 'CYP24A1', 'OTUD3', 'TRIP11', 'MIR500B', 'MIR144', 'CD99P1', 'SPACA6P-AS', 'ADAM20', 'PROSER2', 'FBXL17', 'ASCC2', 'PAX2', 'ARPC4', 'POTED', 'OR2L13', 'MTFR1', 'GPR183', 'WFDC8', 'RPS6KA2', 'UBAC2-AS1', 'SLC35G5', 'KIF21A', 'MIR4734', 'SRGAP2D'}) and 3 missing columns ({'Overall Survival Status', 'Unnamed: 0', 'Overall Survival (Months)'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/VatsalPatel18/Case-Study-HNSCC-ML-Copilot-Agent/hnscc_data/common_genes.23037.sCNV.TCGA.hpvN.scaled.csv (at revision b8311f15ebaabbb33f7f51693118e17f72176d62)
              
              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)