10x H5 Format Error

On most recent commit “c051c44” on v2, the output .h5 files can’t be read by scanpy. Seems to think there’s a key error on ‘genome’?

`KeyError Traceback (most recent call last) ~/utils/miniconda3/envs/scanpy/lib/python3.7/site-packages/scanpy/readwrite.py in _read_v3_10x_h5(filename, start) 253 feature_types=dsets[‘feature_type’].astype(str), –> 254 genome=dsets[‘genome’].astype(str), 255 ),

KeyError: ‘genome’

During handling of the above exception, another exception occurred:

Exception Traceback (most recent call last) <timed exec> in <module>

~/utils/miniconda3/envs/scanpy/lib/python3.7/site-packages/scanpy/readwrite.py in read_10x_h5(filename, genome, gex_only) 159 v3 = ‘/matrix’ in f 160 if v3: –> 161 adata = _read_v3_10x_h5(filename, start=start) 162 if genome: 163 if genome not in adata.var[‘genome’].values:

~/utils/miniconda3/envs/scanpy/lib/python3.7/site-packages/scanpy/readwrite.py in _read_v3_10x_h5(filename, start) 258 return adata 259 except KeyError: –> 260 raise Exception(‘File is missing one or more required datasets.’) 261 262

Exception: File is missing one or more required datasets.`

[letaylor]

Yes - this is it. I can confirm loading the CellBender output in scanpy works just fine when I run CellBender using the h5 input format.

[letaylor]

Ah - I think the error occurs when one is running CellBender using the CellRanger matrix format (a dir with barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) rather than h5 format as input. I am testing out using the CellRanger h5 file now and will report back.