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visiumvignette fails #50

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dimalvovs opened this issue Oct 6, 2023 · 0 comments
Open

visiumvignette fails #50

dimalvovs opened this issue Oct 6, 2023 · 0 comments
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@dimalvovs
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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)
@dimalvovs dimalvovs added the bug Something isn't working label Oct 6, 2023
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