bad anndata object
after last update the pipeline runs without error but the resulting anndata file cannot be imported to Scanpy:
I tested different versions of scanpy with same issue.
adata = scanpy.read_h5ad('./adata.h5ad')
KeyError Traceback (most recent call last)
/home/sguenth/.conda/envs/scRNAseq_analysis_1.6/lib/python3.7/site-packages/anndata/_io/utils.py in func_wrapper(elem, *args, **kwargs)
155 try:
--> 156 return func(elem, *args, **kwargs)
157 except Exception as e:
/home/sguenth/.conda/envs/scRNAseq_analysis_1.6/lib/python3.7/site-packages/anndata/_io/h5ad.py in read_group(group)
531 if encoding_type:
--> 532 EncodingVersions[encoding_type].check(
533 group.name, group.attrs["encoding-version"]
/home/sguenth/.conda/envs/scRNAseq_analysis_1.6/lib/python3.7/enum.py in __getitem__(cls, name)
356 def __getitem__(cls, name):
--> 357 return cls._member_map_[name]
358
KeyError: 'dict'
During handling of the above exception, another exception occurred:
AnnDataReadError Traceback (most recent call last)
<ipython-input-8-a06fda8a8a7f> in <module>()
----> 1 adata = scanpy.read_h5ad('./adata.h5ad')
/home/sguenth/.conda/envs/scRNAseq_analysis_1.6/lib/python3.7/site-packages/anndata/_io/h5ad.py in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
424 d[k] = read_dataframe(f[k])
425 else: # Base case
--> 426 d[k] = read_attribute(f[k])
427
428 d["raw"] = _read_raw(f, as_sparse, rdasp)
/home/sguenth/.conda/envs/scRNAseq_analysis_1.6/lib/python3.7/functools.py in wrapper(*args, **kw)
838 '1 positional argument')
839
--> 840 return dispatch(args[0].__class__)(*args, **kw)
841
842 funcname = getattr(func, '__name__', 'singledispatch function')
/home/sguenth/.conda/envs/scRNAseq_analysis_1.6/lib/python3.7/site-packages/anndata/_io/utils.py in func_wrapper(elem, *args, **kwargs)
161 parent = _get_parent(elem)
162 raise AnnDataReadError(
--> 163 f"Above error raised while reading key {elem.name!r} of "
164 f"type {type(elem)} from {parent}."
165 )
AnnDataReadError: Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.
Edited by Hendrik Schultheis