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to reproduce:
(.env) u88@clarity-3 pycogaps % python visiumvignette.py ______ _____ _____ ___ ______ _____ | ___ \ / __ \ | __ \ / _ \ | ___ \/ ___| | |_/ / _| / \/ ___ | | \// /_\ \| |_/ /\ `--. | __/ | | | | / _ \| | __ | _ || __/ `--. | | | | |_| | \__/\ (_) | |_\ \| | | || | /\__/ / \_| \__, |\____/\___/ \____/\_| |_/\_| \____/ __/ | |___/ Traceback (most recent call last): File "/Users/u88/Documents/jhu/cogaps/pycogaps/visiumvignette.py", line 8, in <module> adata = sc.read_visium(path) File "/Users/u88/Documents/jhu/cogaps/pycogaps/.env/lib/python3.9/site-packages/scanpy/readwrite.py", line 359, in read_visium adata = read_10x_h5(path / count_file, genome=genome) File "/Users/u88/Documents/jhu/cogaps/pycogaps/.env/lib/python3.9/site-packages/scanpy/readwrite.py", line 179, in read_10x_h5 with h5py.File(str(filename), 'r') as f: File "/Users/u88/Documents/jhu/cogaps/pycogaps/.env/lib/python3.9/site-packages/h5py/_hl/files.py", line 567, in __init__ fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr) File "/Users/u88/Documents/jhu/cogaps/pycogaps/.env/lib/python3.9/site-packages/h5py/_hl/files.py", line 231, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 106, in h5py.h5f.open FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'data/VI_116_4/filtered_feature_bc_matrix.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
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to reproduce:
The text was updated successfully, but these errors were encountered: