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Anndata write error in saving uns #409

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Hrovatin opened this issue Jul 31, 2020 · 2 comments
Closed

Anndata write error in saving uns #409

Hrovatin opened this issue Jul 31, 2020 · 2 comments
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@ivirshup

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@Hrovatin
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Hrovatin commented Jul 31, 2020 •
edited by flying-sheep
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I get the below error when trying to save my anndata. The error occurs in uns saving. This does not seem to be the same as #52 as I did not change uns manually since last successfully saving my anndata (I only performed normalisation and HVG selection as suggested in a recent scanpy workshop).

Current uns:

OverloadedDict, wrapping:
	{'doublet_score_filter_colors': array(['#e62e0e', '#a8a8a8'], dtype=object), 'file_colors': array(['#1f77b4', '#ff7f0e', '#2ca02c'], dtype=object), 'log1p': {'base': None}}
With overloaded keys:
	['neighbors'].

The uns when I last successfully saved the object:

OverloadedDict, wrapping:
	{'doublet_score_filter_colors': array(['#e62e0e', '#a8a8a8'], dtype=object), 'file_colors': array(['#1f77b4', '#ff7f0e', '#2ca02c'], dtype=object)}
With overloaded keys:
	['neighbors'].

The error:

adata.write(shared_folder+'data_normalised.h5ad')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-24-1a519bf15528> in <module>
----> 1 adata.write(shared_folder+'data_normalised.h5ad')

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/anndata/_core/anndata.py in write_h5ad(self, filename, compression, compression_opts, force_dense, as_dense)
   1844             filename = self.filename
   1845 
-> 1846         _write_h5ad(
   1847             Path(filename),
   1848             self,

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/anndata/_io/h5ad.py in write_h5ad(filepath, adata, force_dense, as_dense, dataset_kwargs, **kwargs)
    110         write_attribute(f, "varp", adata.varp, dataset_kwargs=dataset_kwargs)
    111         write_attribute(f, "layers", adata.layers, dataset_kwargs=dataset_kwargs)
--> 112         write_attribute(f, "uns", adata.uns, dataset_kwargs=dataset_kwargs)
    113     if adata.isbacked:
    114         adata.file.open(filepath, "r+")

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/h5py/_hl/files.py in __exit__(self, *args)
    459     def __exit__(self, *args):
    460         if self.id:
--> 461             self.close()
    462 
    463     @with_phil

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/h5py/_hl/files.py in close(self)
    441                 for id_ in file_list:
    442                     while id_.valid:
--> 443                         h5i.dec_ref(id_)
    444 
    445                 self.id.close()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5i.pyx in h5py.h5i.dec_ref()

RuntimeError: Can't decrement id ref count (unable to close file, errno = 5, error message = 'Input/output error')
@ivirshup
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ivirshup commented Aug 3, 2020

Thanks for the bug report!

Could you try removing None value from .uns["log1p"]["base"] = None and see if you're able to write then?

@ivirshup ivirshup self-assigned this Aug 3, 2020
@Hrovatin
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Hrovatin commented Aug 3, 2020

Deleting "log1p" from uns does not help.
However, if I try to save it to a different location it works. Could be similar to scverse/scanpy#1351 (comment)?

@Hrovatin Hrovatin closed this as completed Aug 3, 2020
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