Reading 10x scRNA-seq with read_10x_mtx()

I get an error when I use sc.read_10x_mtx() to read scRNA-seq files (matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz) generated by "Illumina HiSeq 4000". The function works fine when I read files generated by other 10x platforms such as "Illumina NovaSeq 6000".

Example:

sc.read_10x_mtx("GSE145328_RAW")

Error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/anaconda3/lib/python3.8/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   3079             try:
-> 3080                 return self._engine.get_loc(casted_key)
   3081             except KeyError as err:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

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: 2

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

KeyError                                  Traceback (most recent call last)
<ipython-input-20-26443e0aed95> in <module>
----> 1 rnaseq1 = sc.read_10x_mtx("GSE145328_RAW")

~/anaconda3/lib/python3.8/site-packages/scanpy/readwrite.py in read_10x_mtx(path, var_names, make_unique, cache, cache_compression, gex_only, prefix)
    479     genefile_exists = (path / f'{prefix}genes.tsv').is_file()
    480     read = _read_legacy_10x_mtx if genefile_exists else _read_v3_10x_mtx
--> 481     adata = read(
    482         str(path),
    483         var_names=var_names,

~/anaconda3/lib/python3.8/site-packages/scanpy/readwrite.py in _read_v3_10x_mtx(path, var_names, make_unique, cache, cache_compression, prefix)
    560     else:
    561         raise ValueError("`var_names` needs to be 'gene_symbols' or 'gene_ids'")
--> 562     adata.var['feature_types'] = genes[2].values
    563     adata.obs_names = pd.read_csv(path / f'{prefix}barcodes.tsv.gz', header=None)[
    564         0

~/anaconda3/lib/python3.8/site-packages/pandas/core/frame.py in __getitem__(self, key)
   3022             if self.columns.nlevels > 1:
   3023                 return self._getitem_multilevel(key)
-> 3024             indexer = self.columns.get_loc(key)
   3025             if is_integer(indexer):
   3026                 indexer = [indexer]

~/anaconda3/lib/python3.8/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   3080                 return self._engine.get_loc(casted_key)
   3081             except KeyError as err:
-> 3082                 raise KeyError(key) from err
   3083 
   3084         if tolerance is not None:

KeyError: 2

Versions

scanpy==1.8.0 anndata==0.7.6 umap==0.5.1 numpy==1.19.2 scipy==1.6.3 pandas==1.2.4 scikit-learn==0.24.2 statsmodels==0.12.2 python-igraph==0.9.1 pynndescent==0.5.2

Start in scanpy/readwrite.py at read_10x_mtx() and _read_v3_10x_mtx(), then compare the HiSeq 4000 features.tsv.gz structure with the files accepted from other 10x platforms. Reproduce the reported KeyError with GSE145328_RAW and verify that the reader handles the input while preserving the expected feature metadata.