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TerryLi710
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lung-methylation-silencing-data

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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 7 new columns ({'strand', 'start', 'gene_type', 'gene_id', 'end', 'tss', 'symbol'}) and 3 missing columns ({'pos', 'probe', 'island_context'}).

This happened while the csv dataset builder was generating data using

hf://datasets/TerryLi710/lung-methylation-silencing-data/lung-methylation-silencing/input/genes.tsv (at revision 6ba7419bdc40e343b920e99f2e6e81a900d840dd), ['hf://datasets/TerryLi710/lung-methylation-silencing-data@6ba7419bdc40e343b920e99f2e6e81a900d840dd/lung-methylation-silencing/input/cpg_annotation.tsv', 'hf://datasets/TerryLi710/lung-methylation-silencing-data@6ba7419bdc40e343b920e99f2e6e81a900d840dd/lung-methylation-silencing/input/genes.tsv', 'hf://datasets/TerryLi710/lung-methylation-silencing-data@6ba7419bdc40e343b920e99f2e6e81a900d840dd/lung-methylation-silencing/input/samples.tsv']

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 1848, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 784, 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 795, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              gene_id: string
              symbol: string
              gene_type: string
              chrom: string
              start: int64
              end: int64
              strand: string
              tss: int64
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1160
              to
              {'probe': Value('string'), 'chrom': Value('string'), 'pos': Value('int64'), 'island_context': 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 1694, 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 1850, 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 7 new columns ({'strand', 'start', 'gene_type', 'gene_id', 'end', 'tss', 'symbol'}) and 3 missing columns ({'pos', 'probe', 'island_context'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/TerryLi710/lung-methylation-silencing-data/lung-methylation-silencing/input/genes.tsv (at revision 6ba7419bdc40e343b920e99f2e6e81a900d840dd), ['hf://datasets/TerryLi710/lung-methylation-silencing-data@6ba7419bdc40e343b920e99f2e6e81a900d840dd/lung-methylation-silencing/input/cpg_annotation.tsv', 'hf://datasets/TerryLi710/lung-methylation-silencing-data@6ba7419bdc40e343b920e99f2e6e81a900d840dd/lung-methylation-silencing/input/genes.tsv', 'hf://datasets/TerryLi710/lung-methylation-silencing-data@6ba7419bdc40e343b920e99f2e6e81a900d840dd/lung-methylation-silencing/input/samples.tsv']
              
              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.

probe string	chrom string	pos int64	island_context string
cg00000292	chr16	28,878,778	shore
cg00000321	chr8	41,310,282	shore
cg00000540	chr1	28,136,152	open_sea
cg00000622	chr15	22,838,619	island
cg00000714	chr19	54,191,826	shore
cg00000734	chr3	129,183,533	island
cg00000769	chr12	123,601,929	island
cg00001245	chr3	15,065,202	island
cg00001446	chr1	43,365,369	shore
cg00001582	chr10	79,068,944	island
cg00001687	chr16	89,695,252	open_sea
cg00001755	chr17	50,869,428	shore
cg00001793	chr12	11,752,455	open_sea
cg00001814	chr2	31,298,093	open_sea
cg00001854	chr16	46,974,579	shore
cg00001997	chr11	108,116,184	open_sea
cg00002028	chr1	20,633,516	island
cg00002080	chr21	29,018,095	shore
cg00002116	chr17	81,703,379	island
cg00002236	chr18	70,205,824	island
cg00002398	chr5	157,520,629	open_sea
cg00002406	chr16	30,355,113	island
cg00002464	chr8	119,416,177	island
cg00002473	chr2	218,124,152	open_sea
cg00002490	chr4	2,262,782	island
cg00002559	chr19	34,428,753	island
cg00002591	chr3	52,836,526	open_sea
cg00002593	chr1	1,333,412	island
cg00002660	chr12	56,189,825	island
cg00002837	chr1	44,047,685	open_sea
cg00002907	chr10	22,540,188	open_sea
cg00003091	chr4	1,713,276	shore
cg00003173	chr3	14,125,249	island
cg00003202	chr1	151,347,035	island
cg00003287	chr1	201,377,020	open_sea
cg00003345	chr1	10,756,441	open_sea
cg00003407	chr17	44,066,801	shore
cg00003513	chr1	10,697,378	shore
cg00003555	chr7	143,288,358	island
cg00003578	chr1	12,540,502	island
cg00003784	chr17	64,506,953	island
cg00003929	chr5	67,189,004	open_sea
cg00003944	chr18	80,036,249	shore
cg00003994	chr7	15,686,236	open_sea
cg00004055	chr16	66,552,841	shore
cg00004072	chr19	39,407,374	island
cg00004082	chr4	10,018,735	shore
cg00004089	chr17	76,682,753	open_sea
cg00004207	chr2	38,750,158	shore
cg00004608	chr6	133,951,324	shore
cg00004723	chr19	19,444,597	open_sea
cg00004818	chr4	177,442,991	shore
cg00004883	chr16	75,114,561	island
cg00004939	chr14	68,794,943	island
cg00004979	chr12	111,447,661	open_sea
cg00004996	chr8	17,414,025	shore
cg00005010	chr16	56,657,936	island
cg00005040	chr6	127,118,060	shore
cg00005077	chr10	45,672,787	island
cg00005083	chr6	46,687,805	island
cg00005112	chr16	69,924,936	open_sea
cg00005297	chr4	3,463,639	island
cg00005306	chr16	30,698,244	island
cg00005325	chr1	201,715,838	open_sea
cg00005354	chr8	27,856,209	open_sea
cg00005423	chr7	150,801,991	shore
cg00005461	chr3	46,089,987	open_sea
cg00005543	chr6	169,751,535	island
cg00005597	chr14	69,636,213	open_sea
cg00005734	chr7	39,622,448	shore
cg00005893	chr6	158,087,510	shore
cg00006032	chr14	66,507,720	island
cg00006122	chr12	52,069,531	shore
cg00006198	chr1	154,503,829	shore
cg00006414	chr7	149,125,744	shore
cg00006884	chr7	23,597,410	island
cg00006899	chr14	103,016,683	open_sea
cg00006948	chr4	1,767,161	island
cg00007076	chr8	66,430,364	shore
cg00007221	chr1	43,533,348	shore
cg00007226	chr14	105,315,028	island
cg00007266	chr17	21,296,455	open_sea
cg00007269	chr19	2,945,107	island
cg00007300	chr14	24,052,224	island
cg00007540	chr14	103,142,927	shelf
cg00007898	chr1	205,211,498	island
cg00007932	chr13	46,597,841	open_sea
cg00007981	chr11	94,129,427	island
cg00007987	chr19	55,645,063	island
cg00008033	chr19	51,926,726	open_sea
cg00008254	chr1	12,616,740	shore
cg00008364	chr17	29,825,841	open_sea
cg00008369	chr22	41,239,788	shore
cg00008387	chr16	50,025,099	island
cg00008665	chr3	43,105,287	shore
cg00008671	chr10	84,328,204	shore
cg00008713	chr18	11,980,953	island
cg00008795	chr16	50,668,201	open_sea
cg00008956	chr2	108,718,669	shore
cg00008971	chr1	45,501,252	shore

End of preview.

lung-methylation-silencing: agent input data

Development copy of the agent-visible input of the Terminal-Bench Science task lung-methylation-silencing, hosted here while the task is under review. Before merge it is mirrored to harborframework/terminal-bench-science-lfs under the same prefix, and this copy is then deleted or made private.

Contents. lung-methylation-silencing/input/: methylation beta values, gene expression, sample table, probe and gene annotation, and a chromatin-state map (6 files, 127 MB). The task image checks every file against environment/data_checksums.sha256 in the task repository. No answers or grading data are stored here.

Source and terms. Derived from public data, with synthetic events added. Sources, citations and the full build are documented in the task's README and authoring/ folder in the Terminal-Bench Science repository.

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