openpipelines-bio / openpipeline

https://openpipelines.bio
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from_h5ad_to_h5mu is failing with 'Unable to synchronously open file (file signature not found)' #586

Closed DriesSchaumont closed 1 year ago

DriesSchaumont commented 1 year ago
Traceback (most recent call last):
  File "/scratch/T96QlO9IXIXMu/b4/f00c4adff1734a511042a2259935d9/.viash_script.sh", line 52, in <module>
    data = { key: anndata.read_h5ad(path) for key, path in zip(par["modality"], par["input"]) }
  File "/scratch/T96QlO9IXIXMu/b4/f00c4adff1734a511042a2259935d9/.viash_script.sh", line 52, in <dictcomp>
    data = { key: anndata.read_h5ad(path) for key, path in zip(par["modality"], par["input"]) }
  File "/usr/local/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 219, in read_h5ad
    with h5py.File(filename, "r") as f:
  File "/usr/local/lib/python3.9/site-packages/h5py/_hl/files.py", line 562, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "/usr/local/lib/python3.9/site-packages/h5py/_hl/files.py", line 235, 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 102, in h5py.h5f.open
OSError: Unable to synchronously open file (file signature not found)
DriesSchaumont commented 1 year ago

Issue was caused by a malformatted file. Closing