Datasets:

VatsalPatel18

/

metabolic-genes-hnscc-sCNV

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 ({'CNGA4', 'LINC00615', 'S1PR2', 'DKK3', 'FMO1', 'MIR4681', 'RHCG', 'MIIP', 'ABCG4', 'HDAC6', 'PPP1R17', 'WDR4', 'DTL', 'MIR4497', 'MRPS7', 'PEAR1', 'IL17C', 'GOLGA8H', 'PIK3R6', 'CHID1', 'LOC100287072', 'TMEM127', 'NCKAP5L', 'MAP3K2', 'SNAR-A10', 'MIR593', 'MARCKS', 'GXYLT2', 'PTGES', 'POLG', 'USP54', 'NUTM2F', 'PAPD4', 'MIR4715', 'DGKB', 'ALG1', 'REG4', 'FAM155B', 'MXI1', 'P2RX3', 'PMS2P3', 'IFT57', 'NLRC4', 'TMCO4', 'CEACAM4', 'LOC100131257', 'PCAT19', 'HIST2H3A', 'QKI', 'MRPL13', 'CNTROB', 'MIR4536-1', 'MED31', 'CSNK1G2', 'NNT-AS1', 'CD37', 'TBXAS1', 'GABBR2', 'RFWD2', 'MYO5A', 'NTNG2', 'TSACC', 'ZNF645', 'FANCL', 'BROX', 'PIWIL4', 'NFS1', 'AOC2', 'MAPT-IT1', 'MRPS6', 'BSN', 'MIR4328', 'SLC2A14', 'BAIAP2', 'ASPHD1', 'NDUFB5', 'KCNAB2', 'TOP2B', 'MTRNR2L3', 'MIR498', 'CLVS2', 'ACTL6B', 'ISG20', 'SLC6A3', 'CHUK', 'OR5D14', 'SNORD105B', 'IL1R2', 'MIR510', 'HHLA2', 'SNORA25', 'DHX36', 'TOR4A', 'OGFR-AS1', 'NDP', 'ADAM8', 'CALCRL', 'ZFPL1', 'SLC39A12', 'GPR31', 'DRD3', 'DNAJA1', 'PGF', 'MIR8078', 'HTR6', 'IFNA7', 'DEFB108B', 'IFRD2', 'PPP1R2P9', 'RECQL4', 'BPGM', 'NSG1', 'POLL', 'H1F0', 'ZNF544', 'CLPTM1', 'TLCD1', 'FLOT1', 'TSPEAR-AS1', 'NEIL3', 'TM2D1', 'REG1B', 'TTC24', 'MBOAT1', 'MIR662', 'ZNF789', 'COX20', 'USF1', 'MIR3682', 'TP53INP1', 'CRYBB2', 'PPM1D', 'ETV5', 'ARMC7', 'GDPD4', 'GJB7', 'SHANK2-AS1', 'ZNF625-ZNF20', 'RAB28', 'FSTL5', 'OR4C46', 'PTPN9', 'SNORD36A', 'CDKN3', 'OR52E8', 'PLAUR', 'MIR3939', 'TIGD7', 'MT1G', 'ATP6V0A4', 'RMST', 'SLCO1B3', 'CAPN1', 'PLEKHM1', '
...
A2', 'TMC2', 'SDF2', 'ACAP2', 'LINC00692', 'LINC00939', 'TMCO6', 'ZNF490', 'RALB', 'SPG7', 'ANKRD13D', 'PCDHGA3', 'MIR4295', 'MVK', 'CECR1', 'GDPD1', 'DHCR7', 'CXXC4', 'LINC00324', 'PRPH2', 'COLGALT1', 'GRK5', 'LINC00323', 'RXFP4', 'FAHD2B', 'MAP10', 'SLC25A5-AS1', 'ANPEP', 'L3MBTL1', 'SRCAP', 'ATG10', 'CD36', 'GPR1', 'MYF5', 'MIR5001', 'COG6', 'GCLC', 'MIR3945HG', 'CAPZA2', 'KRT31', 'LOC643711', 'SEPT4', 'LINC00466', 'TUT1', 'SIAE', 'DRAM2', 'SNRK', 'MNT', 'TPH2', 'USP50', 'ST20-MTHFS', 'TRIP4', 'OGG1', 'TEX14', 'MIR554', 'ZNF658B', 'PRKCG', 'PKD1L2', 'COPE', 'MIR4294', 'MIR1307', 'KRTAP16-1', 'SERP1', 'TMEM126B', 'ADAMTSL4', 'LOC154761', 'CTRB2', 'KALRN', 'LBH', 'TMEM221', 'MIR4287', 'LARGE-AS1', 'REEP3', 'FAM90A1', 'MIR4521', 'TAC3', 'THEM5', 'GNAT3', 'SULT1E1', 'ARHGEF33', 'NAP1L5', 'CANX', 'HSPB8', 'LOC391322', 'VPS13D', 'MYOM2', 'EBP', 'IGFL2', 'PRNCR1', 'RAC1', 'KCNE2', 'SLC8A3', 'UPF1', 'EPPIN', 'TRG-AS1', 'SPRTN', 'ATN1', 'DPY19L1', 'TMEM178A', 'MORC1', 'POLD2', 'TMCC3', 'MIR4532', 'AMZ1', 'TAF9B', 'GPR141', 'MIPEP', 'MIR516B1', 'SNX22', 'ARPC2', 'NFIA', 'ARSA', 'KIAA1324L', 'RPP38', 'MTMR11', 'OR5H2', 'LINC00889', 'RHOBTB3', 'LINC00649', 'PART1', 'SMNDC1', 'FYTTD1', 'CFI', 'LAMTOR4', 'CES2', 'NADK2', 'TONSL', 'VPS8', 'TMED11P', 'DAB1', 'WISP3', 'MTX1', 'GAS5-AS1', 'MMS22L', 'TOE1', 'TNIP3', 'TRIM50', 'KCTD9', 'MIR521-2', 'SH3BGR', 'FOXD2', 'HAT1', 'OR11H6', 'RNF24', 'ZC3H7A', 'PRORSD1P', 'MIR188', 'CREBRF', 'CLDN5', 'OR51G2', 'SNORA38', 'BCL2', 'LINC00851', 'HTR3D'}) and 3 missing columns ({'Unnamed: 0', 'Overall Survival (Months)', 'Overall Survival Status'}).

This happened while the csv dataset builder was generating data using

hf://datasets/VatsalPatel18/metabolic-genes-hnscc-sCNV/common_genes.23037.sCNV.CPTAC.hpvN.scaled.csv (at revision ababb25ad86288e3f2e90acee259626c38385e8c)

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 2013, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, 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 2302, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, 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 1396, 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 1045, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1029, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1124, 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 1884, 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 2015, 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 ({'CNGA4', 'LINC00615', 'S1PR2', 'DKK3', 'FMO1', 'MIR4681', 'RHCG', 'MIIP', 'ABCG4', 'HDAC6', 'PPP1R17', 'WDR4', 'DTL', 'MIR4497', 'MRPS7', 'PEAR1', 'IL17C', 'GOLGA8H', 'PIK3R6', 'CHID1', 'LOC100287072', 'TMEM127', 'NCKAP5L', 'MAP3K2', 'SNAR-A10', 'MIR593', 'MARCKS', 'GXYLT2', 'PTGES', 'POLG', 'USP54', 'NUTM2F', 'PAPD4', 'MIR4715', 'DGKB', 'ALG1', 'REG4', 'FAM155B', 'MXI1', 'P2RX3', 'PMS2P3', 'IFT57', 'NLRC4', 'TMCO4', 'CEACAM4', 'LOC100131257', 'PCAT19', 'HIST2H3A', 'QKI', 'MRPL13', 'CNTROB', 'MIR4536-1', 'MED31', 'CSNK1G2', 'NNT-AS1', 'CD37', 'TBXAS1', 'GABBR2', 'RFWD2', 'MYO5A', 'NTNG2', 'TSACC', 'ZNF645', 'FANCL', 'BROX', 'PIWIL4', 'NFS1', 'AOC2', 'MAPT-IT1', 'MRPS6', 'BSN', 'MIR4328', 'SLC2A14', 'BAIAP2', 'ASPHD1', 'NDUFB5', 'KCNAB2', 'TOP2B', 'MTRNR2L3', 'MIR498', 'CLVS2', 'ACTL6B', 'ISG20', 'SLC6A3', 'CHUK', 'OR5D14', 'SNORD105B', 'IL1R2', 'MIR510', 'HHLA2', 'SNORA25', 'DHX36', 'TOR4A', 'OGFR-AS1', 'NDP', 'ADAM8', 'CALCRL', 'ZFPL1', 'SLC39A12', 'GPR31', 'DRD3', 'DNAJA1', 'PGF', 'MIR8078', 'HTR6', 'IFNA7', 'DEFB108B', 'IFRD2', 'PPP1R2P9', 'RECQL4', 'BPGM', 'NSG1', 'POLL', 'H1F0', 'ZNF544', 'CLPTM1', 'TLCD1', 'FLOT1', 'TSPEAR-AS1', 'NEIL3', 'TM2D1', 'REG1B', 'TTC24', 'MBOAT1', 'MIR662', 'ZNF789', 'COX20', 'USF1', 'MIR3682', 'TP53INP1', 'CRYBB2', 'PPM1D', 'ETV5', 'ARMC7', 'GDPD4', 'GJB7', 'SHANK2-AS1', 'ZNF625-ZNF20', 'RAB28', 'FSTL5', 'OR4C46', 'PTPN9', 'SNORD36A', 'CDKN3', 'OR52E8', 'PLAUR', 'MIR3939', 'TIGD7', 'MT1G', 'ATP6V0A4', 'RMST', 'SLCO1B3', 'CAPN1', 'PLEKHM1', '
              ...
              A2', 'TMC2', 'SDF2', 'ACAP2', 'LINC00692', 'LINC00939', 'TMCO6', 'ZNF490', 'RALB', 'SPG7', 'ANKRD13D', 'PCDHGA3', 'MIR4295', 'MVK', 'CECR1', 'GDPD1', 'DHCR7', 'CXXC4', 'LINC00324', 'PRPH2', 'COLGALT1', 'GRK5', 'LINC00323', 'RXFP4', 'FAHD2B', 'MAP10', 'SLC25A5-AS1', 'ANPEP', 'L3MBTL1', 'SRCAP', 'ATG10', 'CD36', 'GPR1', 'MYF5', 'MIR5001', 'COG6', 'GCLC', 'MIR3945HG', 'CAPZA2', 'KRT31', 'LOC643711', 'SEPT4', 'LINC00466', 'TUT1', 'SIAE', 'DRAM2', 'SNRK', 'MNT', 'TPH2', 'USP50', 'ST20-MTHFS', 'TRIP4', 'OGG1', 'TEX14', 'MIR554', 'ZNF658B', 'PRKCG', 'PKD1L2', 'COPE', 'MIR4294', 'MIR1307', 'KRTAP16-1', 'SERP1', 'TMEM126B', 'ADAMTSL4', 'LOC154761', 'CTRB2', 'KALRN', 'LBH', 'TMEM221', 'MIR4287', 'LARGE-AS1', 'REEP3', 'FAM90A1', 'MIR4521', 'TAC3', 'THEM5', 'GNAT3', 'SULT1E1', 'ARHGEF33', 'NAP1L5', 'CANX', 'HSPB8', 'LOC391322', 'VPS13D', 'MYOM2', 'EBP', 'IGFL2', 'PRNCR1', 'RAC1', 'KCNE2', 'SLC8A3', 'UPF1', 'EPPIN', 'TRG-AS1', 'SPRTN', 'ATN1', 'DPY19L1', 'TMEM178A', 'MORC1', 'POLD2', 'TMCC3', 'MIR4532', 'AMZ1', 'TAF9B', 'GPR141', 'MIPEP', 'MIR516B1', 'SNX22', 'ARPC2', 'NFIA', 'ARSA', 'KIAA1324L', 'RPP38', 'MTMR11', 'OR5H2', 'LINC00889', 'RHOBTB3', 'LINC00649', 'PART1', 'SMNDC1', 'FYTTD1', 'CFI', 'LAMTOR4', 'CES2', 'NADK2', 'TONSL', 'VPS8', 'TMED11P', 'DAB1', 'WISP3', 'MTX1', 'GAS5-AS1', 'MMS22L', 'TOE1', 'TNIP3', 'TRIM50', 'KCTD9', 'MIR521-2', 'SH3BGR', 'FOXD2', 'HAT1', 'OR11H6', 'RNF24', 'ZC3H7A', 'PRORSD1P', 'MIR188', 'CREBRF', 'CLDN5', 'OR51G2', 'SNORA38', 'BCL2', 'LINC00851', 'HTR3D'}) and 3 missing columns ({'Unnamed: 0', 'Overall Survival (Months)', 'Overall Survival Status'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/VatsalPatel18/metabolic-genes-hnscc-sCNV/common_genes.23037.sCNV.CPTAC.hpvN.scaled.csv (at revision ababb25ad86288e3f2e90acee259626c38385e8c)
              
              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)