KeyError: 1 in read_10x_mtx if genes.tsv has only one column

I have a similar issue to this comment.

Carraro=sc.read_10x_mtx('/mnt/Carraro',var_names='gene_ids')

Switching to gene_symbols didn't work

Error messages:

--> This might be very slow. Consider passing `cache=True`, which enables much faster reading from a cache file.

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/miniconda3/envs/flng/lib/python3.8/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   3360             try:
-> 3361                 return self._engine.get_loc(casted_key)
   3362             except KeyError as err:

~/miniconda3/envs/flng/lib/python3.8/site-packages/pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

~/miniconda3/envs/flng/lib/python3.8/site-packages/pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.Int64HashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.Int64HashTable.get_item()

KeyError: 1

The above exception was the direct cause of the following exception:

KeyError                                  Traceback (most recent call last)
/tmp/ipykernel_29519/245170133.py in <module>
----> 1 Carraro=sc.read_10x_mtx('/mnt/Carraro',var_names='gene_ids')

~/miniconda3/envs/flng/lib/python3.8/site-packages/scanpy/readwrite.py in read_10x_mtx(path, var_names, make_unique, cache, cache_compression, gex_only)
    452     genefile_exists = (path / 'genes.tsv').is_file()
    453     read = _read_legacy_10x_mtx if genefile_exists else _read_v3_10x_mtx
--> 454     adata = read(
    455         str(path),
    456         var_names=var_names,

~/miniconda3/envs/flng/lib/python3.8/site-packages/scanpy/readwrite.py in _read_legacy_10x_mtx(path, var_names, make_unique, cache, cache_compression)
    491     elif var_names == 'gene_ids':
    492         adata.var_names = genes[0].values
--> 493         adata.var['gene_symbols'] = genes[1].values
    494     else:
    495         raise ValueError("`var_names` needs to be 'gene_symbols' or 'gene_ids'")

~/miniconda3/envs/flng/lib/python3.8/site-packages/pandas/core/frame.py in __getitem__(self, key)
   3456             if self.columns.nlevels > 1:
   3457                 return self._getitem_multilevel(key)
-> 3458             indexer = self.columns.get_loc(key)
   3459             if is_integer(indexer):
   3460                 indexer = [indexer]

~/miniconda3/envs/flng/lib/python3.8/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   3361                 return self._engine.get_loc(casted_key)
   3362             except KeyError as err:
-> 3363                 raise KeyError(key) from err
   3364 
   3365         if is_scalar(key) and isna(key) and not self.hasnans:

KeyError: 1

Any ideas?

Start in scanpy/readwrite.py, specifically _read_legacy_10x_mtx and the genes.tsv handling shown in the traceback. Reproduce read_10x_mtx with a one-column genes.tsv and check both gene_ids and gene_symbols modes. Done means the input no longer raises KeyError: 1 and the resulting variable names and annotations remain valid.