Hi, I am testing the CellBender according to the official standard procedure, but it reported an error. This seems to be an issue with the input file format. But should this software support h5ad input? I want to know where the problem lies?
Here is my code and error message.
cellbender:remove-background: Command:
cellbender remove-background --input tiny_raw_feature_bc_matrix.h5ad --output tiny_output.h5
cellbender:remove-background: 2023-12-12 11:05:37
cellbender:remove-background: Running remove-background
cellbender:remove-background: Loading data from file tiny_raw_feature_bc_matrix.h5ad
cellbender:remove-background: CellRanger v2 format
/home/user/miniconda/lib/python3.9/site-packages/tables/attributeset.py:291: DataTypeWarning: Unsupported type for attribute 'ordered' in node 'feature_types'. Offending HDF5 class: 8
value = self._g_getattr(self._v_node, name)
/home/user/miniconda/lib/python3.9/site-packages/tables/attributeset.py:291: DataTypeWarning: Unsupported type for attribute 'ordered' in node 'genome'. Offending HDF5 class: 8
value = self._g_getattr(self._v_node, name)
Traceback (most recent call last):
File "/home/user/miniconda/bin/cellbender", line 33, in <module>
sys.exit(load_entry_point('cellbender', 'console_scripts', 'cellbender')())
File "/software/CellBender/cellbender/base_cli.py", line 101, in main
cli_dict[args.tool].run(args)
File "/software/CellBender/cellbender/remove_background/cli.py", line 103, in run
main(args)
File "/software/CellBender/cellbender/remove_background/cli.py", line 196, in main
run_remove_background(args)
File "/software/CellBender/cellbender/remove_background/cli.py", line 145, in run_remove_background
SingleCellRNACountsDataset(input_file=args.input_file,
File "/software/CellBender/cellbender/remove_background/data/dataset.py", line 95, in __init__
self._load_data()
File "/software/CellBender/cellbender/remove_background/data/dataset.py", line 135, in _load_data
self.data = get_matrix_from_cellranger_h5(self.input_file)
File "/software/CellBender/cellbender/remove_background/data/dataset.py", line 1044, in get_matrix_from_cellranger_h5
count_matrix = sp.vstack(csc_list, format='csc')
File "/home/user/miniconda/lib/python3.9/site-packages/scipy/sparse/_construct.py", line 553, in vstack
return bmat([[b] for b in blocks], format=format, dtype=dtype)
File "/home/user/miniconda/lib/python3.9/site-packages/scipy/sparse/_construct.py", line 602, in bmat
raise ValueError('blocks must be 2-D')
ValueError: blocks must be 2-D
Hi, I am testing the CellBender according to the official standard procedure, but it reported an error. This seems to be an issue with the input file format. But should this software support h5ad input? I want to know where the problem lies? Here is my code and error message.