Hello,
I am getting an error when running simple commands like:
import genomepy
# Define genome directory
genome_dir = "data"
# Install mm10
genomepy.install_genome("mm10",provider="ensembl", genomes_dir=genome_dir)
Even when doing
scvi.data.add_dna_sequence(
adata,
chr_var_key="chr",
start_var_key="start",
end_var_key="end",
genome_name="hg19",
genome_dir="data",
)
adata
I get an error in them all.
File /mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/scvi/utils/_dependencies.py:24, in dependencies.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
21 @wraps(fn)
22 def wrapper(*args, **kwargs):
23 error_on_missing_dependencies(*modules)
---> 24 return fn(*args, **kwargs)
File /mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/scvi/data/_preprocessing.py:432, in add_dna_sequence(adata, seq_len, genome_name, genome_dir, genome_provider, install_genome, chr_var_key, start_var_key, end_var_key, sequence_varm_key, code_varm_key)
429 genome_dir = tempdir.name
431 if install_genome:
--> 432 g = genomepy.install_genome(genome_name, genome_provider, genomes_dir=genome_dir)
433 else:
434 g = genomepy.Genome(genome_name, genomes_dir=genome_dir)
...
873 value,
874 ),
875 )
OperationalError: no such column: "size" - should this be a string literal in single-quotes?
or this error:
---------------------------------------------------------------------------
OperationalError Traceback (most recent call last)
Cell In[15], line 7
4 genome_dir = "data"
6 # Install mm10
----> 7 genomepy.install_genome("mm10",provider="ensembl", genomes_dir=genome_dir)
9 # Verify installation
10 genomepy.list_installed_genomes(genomes_dir=genome_dir)
File /mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/functions.py:208, in install_genome(name, provider, genomes_dir, localname, mask, keep_alt, regex, invert_match, bgzip, annotation, only_annotation, skip_matching, skip_filter, threads, force, **kwargs)
206 out_dir = os.path.join(genomes_dir, localname)
207 genome_file = os.path.join(out_dir, f"{localname}.fa")
--> 208 provider = _provider_selection(name, localname, genomes_dir, provider)
210 # check which files need to be downloaded
211 genome_found = _is_genome_dir(out_dir)
File /mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/functions.py:371, in _provider_selection(name, localname, genomes_dir, provider)
368 if p in ["ensembl", "ucsc", "ncbi"]:
369 provider = p
--> 371 return _lazy_provider_selection(name, provider)
File /mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/functions.py:342, in _lazy_provider_selection(name, provider)
340 """return the first PROVIDER which has genome NAME"""
341 providers = []
--> 342 for p in online_providers(provider):
...
873 value,
874 ),
875 )
OperationalError: no such column: "size" - should this be a string literal in single-quotes?
Or even in the terminal:
$ genomepy search zebrafish
00:05:02 | INFO | Downloading assembly summaries from GENCODE
Traceback (most recent call last):
File "/mnt/RAID5/miniforge/envs/scvi-env/bin/genomepy", line 10, in <module>
sys.exit(cli())
^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/cli.py", line 412, in search
for row in genomepy.search(term, provider, exact, size):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/providers/__init__.py", line 135, in search
for p in online_providers(provider):
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/providers/__init__.py", line 104, in online_providers
yield create(provider)
^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/providers/__init__.py", line 60, in create
return p()
^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/providers/gencode.py", line 41, in __init__
self.genomes = _get_genomes(self._url)
^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/genomepy/providers/gencode.py", line 249, in _get_genomes
genomes = get_genomes(ftp_link)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/contextlib.py", line 81, in inner
return func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/diskcache/core.py", line 1877, in wrapper
self.set(key, result, expire, tag=tag, retry=True)
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/diskcache/core.py", line 808, in set
self._row_insert(db_key, raw, now, columns)
File "/mnt/RAID5/miniforge/envs/scvi-env/lib/python3.12/site-packages/diskcache/core.py", line 857, in _row_insert
sql(
sqlite3.OperationalError: no such column: "size" - should this be a string literal in single-quotes?
any ideas on how I can fix this to run scvi?