Datasets:

luoyiming1991
/

vep113-grch38-reference-bundle

Error code:   DatasetGenerationError
Exception:    TypeError
Message:      int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1531, in _prepare_split_single
                  for key, record in generator:
                                     ^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
                  for item in generator(*args, **kwargs):
                              ~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 127, in _generate_examples
                  for example_idx, example in enumerate(self._get_pipeline_from_tar(tar_path, tar_iterator)):
                                              ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/webdataset/webdataset.py", line 32, in _get_pipeline_from_tar
                  for filename, f in tar_iterator:
                                     ^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/track.py", line 49, in __iter__
                  for x in self.generator(*self.args):
                           ~~~~~~~~~~~~~~^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 1405, in _iter_from_urlpath
                  with xopen(urlpath, "rb", download_config=download_config, block_size=0) as f:
                       ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 982, in xopen
                  file_obj = fs.open(paths[0], mode)
                File "<string>", line 3, in open
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1176, in __call__
                  return self._mock_call(*args, **kwargs)
                         ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1180, in _mock_call
                  return self._execute_mock_call(*args, **kwargs)
                         ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/unittest/mock.py", line 1247, in _execute_mock_call
                  result = effect(*args, **kwargs)
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 786, in wrapped
                  tracker.files[urlpath] = {"read": 0, "size": int(f.size)}
                                                               ~~~^^^^^^^^
              TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
              
              The above exception was the direct cause of the following exception:
              
              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 1393, 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 1571, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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.

gz unknown	__key__ string	__url__ string
"cHN0MAUKAwAAAAEEAgAABNkEERhCaW86OkVuc0VNQkw6OlRyYW5zY3JpcHQDAAAAIgiRAAAAEWNkbmFfY29kaW5nX3N0YXJ0Cg9(...TRUNCATED)	homo_sapiens/113_GRCh38/1/1-1000000	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAwAAAAEEAgAAANkEEShCaW86OkVuc0VNQkw6OkZ1bmNnZW46OlJlZ3VsYXRvcnlGZWF0dXJlAwAAAA0EAwA(...TRUNCATED)	homo_sapiens/113_GRCh38/1/1-1000000_reg	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAgAAAIUEERhCaW86OkVuc0VNQkw6OlRyYW5zY3JpcHQDAAAAIQoPRU5TRzAwMDAwMTE3NjIwAAAAD19nZW5(...TRUNCATED)	homo_sapiens/113_GRCh38/1/100000001-101000000	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAwAAAAEEAgAAAIQEEShCaW86OkVuc0VNQkw6OkZ1bmNnZW46OlJlZ3VsYXRvcnlGZWF0dXJlAwAAAA0KCGV(...TRUNCATED)	homo_sapiens/113_GRCh38/1/100000001-101000000_reg	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAgAAAGUEERhCaW86OkVuc0VNQkw6OlRyYW5zY3JpcHQDAAAAHQoKSEdOQzozNTcyOAAAAA1fZ2VuZV9oZ25(...TRUNCATED)	homo_sapiens/113_GRCh38/1/10000001-11000000	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAwAAAAEEAgAAANQEEShCaW86OkVuc0VNQkw6OkZ1bmNnZW46OlJlZ3VsYXRvcnlGZWF0dXJlAwAAAA0JAAA(...TRUNCATED)	homo_sapiens/113_GRCh38/1/10000001-11000000_reg	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAgAAAp4EERhCaW86OkVuc0VNQkw6OlRyYW5zY3JpcHQDAAAAIgoLTk1fMDE3OTcxLjQAAAAHX3JlZnNlcQQ(...TRUNCATED)	homo_sapiens/113_GRCh38/1/1000001-2000000	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAwAAAAEEAgAAAWYEEShCaW86OkVuc0VNQkw6OkZ1bmNnZW46OlJlZ3VsYXRvcnlGZWF0dXJlAwAAAA0KEVJ(...TRUNCATED)	homo_sapiens/113_GRCh38/1/1000001-2000000_reg	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAgAAAJQEERhCaW86OkVuc0VNQkw6OlRyYW5zY3JpcHQDAAAAIQUAAAALdHJhbnNsYXRpb24IgQAAAAd2ZXJ(...TRUNCATED)	homo_sapiens/113_GRCh38/1/101000001-102000000	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)
"cHN0MAUKAwAAAAEEAwAAAAEEAgAAAGUEEShCaW86OkVuc0VNQkw6OkZ1bmNnZW46OlJlZ3VsYXRvcnlGZWF0dXJlAwAAAA0KDEV(...TRUNCATED)	homo_sapiens/113_GRCh38/1/101000001-102000000_reg	"hf://datasets/luoyiming1991/vep113-grch38-reference-bundle@6871304a80b58775569d9f5adb73a23acd78c2dd(...TRUNCATED)

End of preview.

VEP 113 / GRCh38 reference bundle — cache, FASTA, LOFTEE data

A fast mirror of the reference data needed to run Ensembl VEP release 113 offline on GRCh38, in the prepared forms a local annotation pipeline needs — assembled for the WES/WGS diagnostic analysis pipeline (IEI variant-review workbench), whose downloader verifies every file against pinned SHA-256 checksums and falls back to the canonical sources automatically.

Mirror rationale: the canonical servers often serve well under 1 MiB/s per connection transatlantically; this mirror typically saves hours on first-time setup. Contents are unmodified from their sources except where noted.

Files

File	Contents	Source
`homo_sapiens_vep_113_GRCh38.cache.tar.gz`	Ensembl VEP indexed cache, release 113, GRCh38 (retarred from the extracted official cache)	Ensembl
`Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz` (+ `.fai`, `.gzi`)	GRCh38 primary-assembly FASTA, re-compressed as BGZF with indexes (VEP/LOFTEE require BGZF; Ensembl ships plain gzip)	Ensembl
`human_ancestor.fa.gz` (+ `.fai`, `.gzi`)	LOFTEE GRCh38 ancestral sequence	LOFTEE (Broad)
`loftee.sql`	LOFTEE GRCh38 conservation database	LOFTEE (Broad)
`gerp_conservation_scores.homo_sapiens.GRCh38.bw`	GERP conservation bigWig for LOFTEE GRCh38	Ensembl/LOFTEE

Licensing and attribution

Ensembl data (VEP cache, FASTA, GERP bigWig): Ensembl data are freely available without restriction; see https://www.ensembl.org/info/about/legal/disclaimer.html. Cite: McLaren et al., The Ensembl Variant Effect Predictor, Genome Biology 17, 122 (2016), and the current Ensembl release paper.
LOFTEE data (ancestral FASTA, conservation SQL): from the public LOFTEE resources (MIT-licensed project); cite Karczewski et al., Nature 581, 434–443 (2020). https://github.com/konradjk/loftee
This compilation adds no restrictions.

Use with the pipeline

scripts/download_references.sh uses this mirror automatically when configured, verifying each file against the SHA-256 checksums pinned in the script and falling back to the canonical Ensembl/Broad sources if the mirror is unavailable or fails verification. Manual use: download, verify, then place the files under your configured reference locations (vep_cache/ for the extracted tarball, fasta/, loftee/).

Downloads last month: 37

Total file size:

39.5 GB