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Illegal slicing argument for scalar dataspace when attempting to read 10x_h5 with version 1.9.0
Hi
When attempting so simply read a h5 file with:
Python version - 3.8.8
# results_file = path to 10X h5 file
# adata = sc.read_10x_h5(results_file)
I get the following error which is fixed when rolling back to scanpy=1.8.2
ValueError Traceback (most recent call last)
<ipython-input-3-8ddd0a13aab2> in <module>
8 print(results_file)
----> 9 adata = sc.read_10x_h5(results_file)
10 adata.var_names_make_unique()
11 adata.obs.index = meta.iloc[idx,2] + '-' + adata.obs.index
/opt/conda/lib/python3.8/site-packages/scanpy/readwrite.py in read_10x_h5(filename, genome, gex_only, backup_url)
181 v3 = '/matrix' in f
182 if v3:
--> 183 adata = _read_v3_10x_h5(filename, start=start)
184 if genome:
185 if genome not in adata.var['genome'].values:
/opt/conda/lib/python3.8/site-packages/scanpy/readwrite.py in _read_v3_10x_h5(filename, start)
266 try:
267 dsets = {}
--> 268 _collect_datasets(dsets, f["matrix"])
269
270 from scipy.sparse import csr_matrix
/opt/conda/lib/python3.8/site-packages/scanpy/readwrite.py in _collect_datasets(dsets, group)
254 for k, v in group.items():
255 if isinstance(v, h5py.Dataset):
--> 256 dsets[k] = v[:]
257 else:
258 _collect_datasets(dsets, v)
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
/opt/conda/lib/python3.8/site-packages/h5py/_hl/dataset.py in __getitem__(self, args, new_dtype)
767 if self.shape == ():
768 fspace = self.id.get_space()
--> 769 selection = sel2.select_read(fspace, args)
770 if selection.mshape is None:
771 arr = numpy.ndarray((), dtype=new_dtype)
/opt/conda/lib/python3.8/site-packages/h5py/_hl/selections2.py in select_read(fspace, args)
99 """
100 if fspace.shape == ():
--> 101 return ScalarReadSelection(fspace, args)
102
103 raise NotImplementedError()
/opt/conda/lib/python3.8/site-packages/h5py/_hl/selections2.py in __init__(self, fspace, args)
84 self.mshape = ()
85 else:
---> 86 raise ValueError("Illegal slicing argument for scalar dataspace")
87
88 self.mspace = h5s.create(h5s.SCALAR)
ValueError: Illegal slicing argument for scalar dataspace
Thanks!!
Nadav
Can you share the output of sc.logging.print_versions() in the environment that's causing you problems?
I'm unable to reproduce with recent cellranger outputs.
Hey sorry for the delay:
-----
anndata 0.7.5
scanpy 1.9.0
-----
PIL 8.1.2
anyio NA
attr 20.3.0
babel 2.9.0
backcall 0.2.0
brotli NA
cairo 1.20.0
certifi 2020.12.05
cffi 1.14.5
chardet 4.0.0
cloudpickle 1.6.0
colorama 0.4.4
cycler 0.10.0
cython_runtime NA
cytoolz 0.11.0
dask 2021.03.1
dateutil 2.8.1
decorator 4.4.2
fsspec 0.8.7
google NA
h5py 3.1.0
idna 2.10
igraph 0.8.3
ipykernel 5.5.0
ipython_genutils 0.2.0
jedi 0.18.0
jinja2 2.11.3
joblib 1.0.1
json5 NA
jsonschema 3.2.0
jupyter_server 1.4.1
jupyterlab_server 2.3.0
kiwisolver 1.3.1
leidenalg 0.8.3
llvmlite 0.34.0
louvain 0.7.0
markupsafe 1.1.1
matplotlib 3.3.4
mpl_toolkits NA
natsort 7.1.1
nbclassic NA
nbformat 5.1.2
numba 0.51.2
numpy 1.20.1
packaging 20.9
pandas 1.2.3
parso 0.8.1
pexpect 4.8.0
pickleshare 0.7.5
pkg_resources NA
prometheus_client NA
prompt_toolkit 3.0.16
psutil 5.8.0
ptyprocess 0.7.0
pvectorc NA
pyarrow 0.16.0
pygments 2.8.0
pyparsing 2.4.7
pyrsistent NA
pytoml NA
pytz 2021.1
requests 2.25.1
ruamel NA
scipy 1.6.1
send2trash NA
session_info 1.0.0
setuptools_scm NA
six 1.15.0
sklearn 0.24.1
sniffio 1.2.0
socks 1.7.1
sphinxcontrib NA
storemagic NA
tblib 1.7.0
texttable 1.6.3
tlz 0.11.0
toolz 0.11.1
tornado 6.1
traitlets 5.0.5
typing_extensions NA
urllib3 1.26.3
wcwidth 0.2.5
yaml 5.3.1
zmq 22.0.3
-----
IPython 7.21.0
jupyter_client 6.1.11
jupyter_core 4.7.1
jupyterlab 3.0.9
notebook 6.2.0
-----
Python 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27) [GCC 9.3.0]
Linux-4.15.0-112-generic-x86_64-with-glibc2.10
-----
Session information updated at 2022-04-08 14:58
I got similar error when I was trying to use .h5 file from cellbender output. I have multiome data.
`>>> adata = scanpy.read_10x_h5("/sc/arion/projects/hmDNAmap/snHeroin/analysis/ARC_TD005235-354/outs/cellbender/cb_feature_bc_matrix_filtered.h5", gex_only=False)`
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/scanpy/readwrite.py", line 183, in read_10x_h5
adata = _read_v3_10x_h5(filename, start=start)
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/scanpy/readwrite.py", line 268, in _read_v3_10x_h5
_collect_datasets(dsets, f["matrix"])
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/scanpy/readwrite.py", line 256, in _collect_datasets
dsets[k] = v[:]
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 "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/h5py/_hl/dataset.py", line 738, in __getitem__
selection = sel2.select_read(fspace, args)
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/h5py/_hl/selections2.py", line 101, in select_read
return ScalarReadSelection(fspace, args)
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/h5py/_hl/selections2.py", line 86, in __init__
raise ValueError("Illegal slicing argument for scalar dataspace")
> **ValueError: Illegal slicing argument for scalar dataspace**
>>> scanpy.logging.print_versions()
anndata 0.8.0 scanpy 1.9.1
PIL 8.4.0 beta_ufunc NA binom_ufunc NA bottleneck 1.3.2 cffi 1.14.6 cloudpickle 2.0.0 colorama 0.4.4 concurrent NA cycler 0.10.0 cython_runtime NA cytoolz 0.11.0 dask 2021.10.0 dateutil 2.8.2 defusedxml 0.7.1 encodings NA fsspec 2021.08.1 genericpath NA h5py 3.3.0 igraph 0.9.6 jinja2 2.11.3 joblib 1.1.0 kiwisolver 1.3.1 leidenalg 0.8.7 llvmlite 0.37.0 markupsafe 1.1.1 matplotlib 3.4.3 mkl 2.4.0 mpl_toolkits NA natsort 7.1.1 nbinom_ufunc NA ntpath NA numba 0.54.1 numexpr 2.7.3 numpy 1.20.3 opcode NA packaging 21.0 pandas 1.3.4 pkg_resources NA posixpath NA psutil 5.8.0 pyexpat NA pyparsing 3.0.4 pytz 2021.3 scipy 1.7.1 scrublet NA session_info 1.0.0 six 1.16.0 sklearn 0.24.2 sphinxcontrib NA sre_compile NA sre_constants NA sre_parse NA tblib 1.7.0 texttable 1.6.4 tlz 0.11.0 toolz 0.11.1 typing_extensions NA wcwidth 0.2.5 yaml 6.0 zope NA
Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-glibc2.17
Session information updated at 2022-05-17 14:56
I'm getting the same error using the CellBender tutorial output. Attaching the file to make it easier to reproduce.
sc.logging.print_versions()
-----
anndata 0.7.8
scanpy 1.9.1
-----
PIL 9.0.1
asttokens NA
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
cffi 1.15.0
cycler 0.10.0
cython_runtime NA
dateutil 2.8.2
debugpy 1.6.0
decorator 5.1.1
defusedxml 0.7.1
doubletdetection 4.2
entrypoints 0.4
executing 0.8.3
google NA
h5py 3.6.0
hypergeom_ufunc NA
igraph 0.9.9
ipykernel 6.10.0
ipython_genutils 0.2.0
ipywidgets 7.7.0
jedi 0.18.1
joblib 1.1.0
kiwisolver 1.4.2
leidenalg 0.8.9
llvmlite 0.38.0
louvain 0.7.1
matplotlib 3.5.1
matplotlib_inline NA
mkl 2.4.0
mpl_toolkits NA
mudata 0.1.1
muon 0.1.2
natsort 8.1.0
nbinom_ufunc NA
numba 0.55.1
numexpr 2.8.1
numpy 1.21.2
organize_metadata NA
packaging 21.3
pandas 1.4.1
parso 0.8.3
pexpect 4.8.0
phenograph 1.5.7
pickleshare 0.7.5
pkg_resources NA
prompt_toolkit 3.0.28
psutil 5.9.0
ptyprocess 0.7.0
pure_eval 0.2.2
pycparser 2.21
pydev_ipython NA
pydevconsole NA
pydevd 2.8.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.11.2
pynndescent 0.5.6
pyparsing 3.0.7
pytz 2022.1
scikits NA
scipy 1.8.0
seaborn 0.11.2
session_info 1.0.0
setuptools 62.0.0
setuptools_scm NA
six 1.16.0
sklearn 1.0.2
stack_data 0.2.0
statsmodels 0.13.2
tables 3.7.0
texttable 1.6.4
threadpoolctl 3.1.0
tornado 6.1
tqdm 4.63.1
traitlets 5.1.1
typing_extensions NA
umap 0.5.2
wcwidth 0.2.5
yaml 6.0
zipp NA
zmq 22.3.0
-----
IPython 8.2.0
jupyter_client 7.1.2
jupyter_core 4.9.2
notebook 6.4.10
-----
Python 3.9.11 (main, Mar 28 2022, 10:10:35) [GCC 7.5.0]
Linux-4.15.0-142-generic-x86_64-with-glibc2.27
-----
Session information updated at 2022-05-24 15:05
Was this fixed by https://github.com/scverse/scanpy/pull/2344 ? Edit: Yes
