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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 9 new columns ({'locus', 'duplicate_count', 'd_call', 'junction_aa', 'j_call', 'sequence_id', 'v_call', 'junction', 'duplicate_frequency'}) and 19 missing columns ({'vaccine', 'cell_subset', 'chain', 'reads', 'HLA-C_1', 'donor', 'HLA-B_1', 'sample_id', 'HLA-B_2', 'file_name', 'timepoint', 'raw_filename', 'day', 'season', 'HLA-A_2', 'HLA-C_2', 'HLA-A_1', 'clonotypes', 'replicate'}).
This happened while the csv dataset builder was generating data using
gzip://YB13_0_F.airr.tsv::hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_0_F.airr.tsv.gz, ['hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/metadata.tsv', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_0_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_12_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_45_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_5_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_pre0_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_0_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_0_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_12_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_12_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_45_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_45_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_5_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_5_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_pre0_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_pre0_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB16_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB16_F2.airr.tsv.gz']
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
sequence_id: int64
duplicate_count: int64
duplicate_frequency: double
locus: string
v_call: string
d_call: double
j_call: string
junction: string
junction_aa: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1350
to
{'file_name': Value('string'), 'sample_id': Value('string'), 'donor': Value('string'), 'vaccine': Value('string'), 'season': Value('int64'), 'timepoint': Value('string'), 'day': Value('float64'), 'cell_subset': Value('string'), 'replicate': Value('string'), 'chain': Value('string'), 'reads': Value('int64'), 'clonotypes': Value('int64'), 'HLA-A_1': Value('string'), 'HLA-A_2': Value('string'), 'HLA-B_1': Value('string'), 'HLA-B_2': Value('string'), 'HLA-C_1': Value('string'), 'HLA-C_2': Value('string'), 'raw_filename': 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 9 new columns ({'locus', 'duplicate_count', 'd_call', 'junction_aa', 'j_call', 'sequence_id', 'v_call', 'junction', 'duplicate_frequency'}) and 19 missing columns ({'vaccine', 'cell_subset', 'chain', 'reads', 'HLA-C_1', 'donor', 'HLA-B_1', 'sample_id', 'HLA-B_2', 'file_name', 'timepoint', 'raw_filename', 'day', 'season', 'HLA-A_2', 'HLA-C_2', 'HLA-A_1', 'clonotypes', 'replicate'}).
This happened while the csv dataset builder was generating data using
gzip://YB13_0_F.airr.tsv::hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_0_F.airr.tsv.gz, ['hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/metadata.tsv', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_0_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_12_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_45_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_5_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB13_pre0_F.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_0_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_0_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_12_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_12_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_45_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_45_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_5_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_5_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_pre0_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB14_pre0_F2.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB16_F1.airr.tsv.gz', 'hf://datasets/isalgo/airr_flu_vac@61e3c4cb9f39b28380aee4434f182b6c119d0981/samples/YB16_F2.airr.tsv.gz']
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.
file_name string | sample_id string | donor string | vaccine string | season int64 | timepoint string | day float64 | cell_subset string | replicate null | chain string | reads int64 | clonotypes int64 | HLA-A_1 string | HLA-A_2 string | HLA-B_1 string | HLA-B_2 string | HLA-C_1 string | HLA-C_2 string | raw_filename string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
YB13_0_F.airr.tsv.gz | YB13_0_F | YB | influenza subunit inactivated (Influvac, trivalent) | 13 | 0 | 0 | bulk | null | TRB | 5,999 | 4,888 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB13_0_F.TRB.tsv.gz |
YB13_12_F.airr.tsv.gz | YB13_12_F | YB | influenza subunit inactivated (Influvac, trivalent) | 13 | 12 | 12 | bulk | null | TRB | 165,477 | 102,290 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB13_12_F.TRB.tsv.gz |
YB13_45_F.airr.tsv.gz | YB13_45_F | YB | influenza subunit inactivated (Influvac, trivalent) | 13 | 45 | 45 | bulk | null | TRB | 694,401 | 356,332 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB13_45_F.TRB.tsv.gz |
YB13_5_F.airr.tsv.gz | YB13_5_F | YB | influenza subunit inactivated (Influvac, trivalent) | 13 | 5 | 5 | bulk | null | TRB | 225,145 | 129,507 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB13_5_F.TRB.tsv.gz |
YB13_pre0_F.airr.tsv.gz | YB13_pre0_F | YB | influenza subunit inactivated (Influvac, trivalent) | 13 | pre0 | -14 | bulk | null | TRB | 130,503 | 81,303 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB13_pre0_F.TRB.tsv.gz |
YB14_0_F1.airr.tsv.gz | YB14_0_F1 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 0 | 0 | bulk | null | TRB | 958,919 | 464,357 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_0_F1.TRB.tsv.gz |
YB14_0_F2.airr.tsv.gz | YB14_0_F2 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 0 | 0 | bulk | null | TRB | 1,297,389 | 572,391 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_0_F2.TRB.tsv.gz |
YB14_12_F1.airr.tsv.gz | YB14_12_F1 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 12 | 12 | bulk | null | TRB | 1,432,617 | 600,656 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_12_F1.TRB.tsv.gz |
YB14_12_F2.airr.tsv.gz | YB14_12_F2 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 12 | 12 | bulk | null | TRB | 1,295,898 | 550,928 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_12_F2.TRB.tsv.gz |
YB14_45_F1.airr.tsv.gz | YB14_45_F1 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 45 | 45 | bulk | null | TRB | 990,639 | 433,869 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_45_F1.TRB.tsv.gz |
YB14_45_F2.airr.tsv.gz | YB14_45_F2 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 45 | 45 | bulk | null | TRB | 936,249 | 415,121 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_45_F2.TRB.tsv.gz |
YB14_5_F1.airr.tsv.gz | YB14_5_F1 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 5 | 5 | bulk | null | TRB | 2,702,711 | 887,146 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_5_F1.TRB.tsv.gz |
YB14_5_F2.airr.tsv.gz | YB14_5_F2 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | 5 | 5 | bulk | null | TRB | 2,765,740 | 915,796 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_5_F2.TRB.tsv.gz |
YB14_pre0_F1.airr.tsv.gz | YB14_pre0_F1 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | pre0 | -14 | bulk | null | TRB | 1,476,779 | 665,011 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_pre0_F1.TRB.tsv.gz |
YB14_pre0_F2.airr.tsv.gz | YB14_pre0_F2 | YB | influenza subunit inactivated (Influvac, trivalent) | 14 | pre0 | -14 | bulk | null | TRB | 1,464,037 | 632,096 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB14_pre0_F2.TRB.tsv.gz |
YB16_F1.airr.tsv.gz | YB16_F1 | YB | influenza subunit inactivated (Influvac, trivalent) | 16 | null | null | bulk | null | TRB | 1,379,711 | 516,784 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB16_F1.TRB.tsv.gz |
YB16_F2.airr.tsv.gz | YB16_F2 | YB | influenza subunit inactivated (Influvac, trivalent) | 16 | null | null | bulk | null | TRB | 1,382,886 | 522,276 | A*03:02:01 | A*31:01:02 | B*18:01:01 | B*18:17N | C*12:03:01 | C*15:02:01 | YB16_F2.TRB.tsv.gz |
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End of preview.
Influenza subunit vaccine — longitudinal TCRβ repertoires
Deep TCRβ repertoire time-course of one healthy volunteer vaccinated with trivalent subunit
inactivated influenza vaccine (Influvac) across three annual seasons, sampled before and after each
vaccination. A companion vaccine cohort to isalgo/airr_yfv19 (yellow fever) — but with a deliberately
weak response: the paper's finding is that only a limited number of new memory T-cell clones are
recruited per seasonal vaccination (peaking ~day 45).
Cite as — Sycheva AL, Pogorelyy MV, Komech EA, Minervina AA, Zvyagin IV, Staroverov DB, Chudakov DM, Lebedev YB, Mamedov IZ. "Quantitative profiling reveals minor changes of T cell receptor repertoire in response to subunit inactivated influenza vaccine." Vaccine 2018;36(12):1599–1605. DOI 10.1016/j.vaccine.2018.02.027 · PMID 29454515 · raw reads SRA SRP111073.
Contents
| File | What |
|---|---|
samples/<sample_id>.airr.tsv.gz |
17 per-sample AIRR TRB clonotype tables (UMI-corrected) |
metadata.tsv |
one row per sample (donor, season, timepoint, subset, reads, HLA) |
Clonotype tables (samples/*.airr.tsv.gz)
Tab-separated AIRR Rearrangement export, one clonotype per row:
sequence_id, duplicate_count, duplicate_frequency, locus, v_call, d_call, j_call, junction, junction_aa.
duplicate_countis the UMI-corrected molecule count — the abundance to use;duplicate_frequencyis its within-sample fraction.junction/junction_aaare the anchor-included CDR3 (conserved Cys104 … Phe/Trp118), i.e. AIRR junction, not the anchor-excluded IMGTcdr3.v_call/j_callare gene-level IMGT names (TRBV29-1); the reanalysis export carries no allele resolution, so none is fabricated.d_callis empty (not resolved for TRB here).
Converted from the source UMI-corrected MiXCR export (cloneId, uniqueMoleculeCount, uniqueMoleculeFraction, nSeqCDR3, aaSeqCDR3, bestVGene, bestJGene).
metadata.tsv
Key file_name (= the samples/ basename). Columns:
- design —
sample_id,donor(YB, a single volunteer),season(13/14/16= vaccination year),timepoint(pre0/0/5/12/45),day(−14/0/5/12/45;pre0= day −14),cell_subset(bulk),replicate(F1/F2biological replicates, blank for single),chain(TRB). - depth —
reads(ΣuniqueMoleculeCount),clonotypes(rows). - HLA class I —
HLA-A_1, HLA-A_2, HLA-B_1, HLA-B_2, HLA-C_1, HLA-C_2(donor YB's germline typing;HLA-Cwas typed at low resolution — representative allele shown).
Notes / caveats
- Single donor across 3 seasons — HLA is one genotype;
seasonis the longitudinal axis. - Shipped tables are the UMI-corrected reanalysis (bulk
F/F1/F2). The original submission also has sorted memory (M) fractions (not in this reanalysis set); available on request. - Response is weak by design (see the paper) — a hard benchmark for detecting vaccine-induced clones.
Usage
Each samples/*.airr.tsv.gz is a gzipped AIRR-Rearrangement TSV; metadata.tsv keys them by
file_name. Load with any TSV reader (e.g. pandas.read_csv(..., sep="\t")).
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