error when loading oracle data
heroineray opened this issue · 1 comments
heroineray commented
Hello! Thank you for creating this wonderful package!
I found an error when using oracle = co.data.load_tutorial_oracle_object(). How can I solve this problem?
Found serious error when loading data. It might be because of discrepancy of dependent library. You are trying to load an object which was generated with a library of different version.
Traceback (most recent call last):
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/celloracle/trajectory/oracle_core.py", line 71, in load_oracle
obj = load_hdf5(filename=file_path, obj_class=Oracle, ignore_attrs_if_err=["knn", "knn_smoothing_w", "pca"])
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/celloracle/utility/hdf5_processing.py", line 122, in load_hdf5
_file = h5py.File(filename, "r")
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/h5py/_hl/files.py", line 567, in __init__
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/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
OSError: Unable to open file (truncated file: eof = 409600, sblock->base_addr = 0, stored_eof = 81507062)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/IPython/core/interactiveshell.py", line 3508, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-4-2eef2d105f79>", line 1, in <module>
oracle = co.data.load_tutorial_oracle_object()
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/celloracle/data/load_data.py", line 118, in load_tutorial_oracle_object
return load_hdf5.load_hdf5(path)
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/celloracle/utility/load_hdf5.py", line 35, in load_hdf5
obj = load_oracle(file_path=file_path)
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/celloracle/trajectory/oracle_core.py", line 75, in load_oracle
obj = load_hdf5(filename=file_path, obj_class=Oracle, ignore_attrs_if_err=["knn", "knn_smoothing_w", "pca"])
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/celloracle/utility/hdf5_processing.py", line 122, in load_hdf5
_file = h5py.File(filename, "r")
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/site-packages/h5py/_hl/files.py", line 567, in __init__
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
File "/home/ray/anaconda3/envs/celloracle_env/lib/python3.8/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
OSError: Unable to open file (truncated file: eof = 409600, sblock->base_addr = 0, stored_eof = 81507062
Session information:
Package Version
------------------------- --------
anndata 0.9.1
anyio 3.7.1
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.3
asttokens 2.2.1
attrs 23.1.0
backcall 0.2.0
beautifulsoup4 4.12.2
biofluff 3.0.4
biopython 1.81
biothings-client 0.2.6
bleach 6.0.0
boltons 23.0.0
Brotli 1.0.9
cachetools 5.3.1
cattrs 23.1.2
celloracle 0.14.0
certifi 2023.5.7
cffi 1.15.1
charset-normalizer 3.2.0
click 8.1.4
colorama 0.4.6
comm 0.1.3
conda 23.5.0
conda-package-handling 2.0.2
conda_package_streaming 0.8.0
configparser 5.3.0
contourpy 1.1.0
cryptography 39.0.0
cycler 0.11.0
Cython 0.29.36
debugpy 1.6.7
decorator 5.1.1
defusedxml 0.7.1
diskcache 5.6.1
dnspython 2.3.0
docopt 0.6.2
et-xmlfile 1.1.0
exceptiongroup 1.1.2
executing 1.2.0
fastjsonschema 2.17.1
feather-format 0.4.1
filelock 3.12.2
fonttools 4.40.0
fqdn 1.5.1
frozendict 2.3.8
genomepy 0.16.1
gimmemotifs 0.17.0
goatools 1.3.1
h5py 3.9.0
HTSeq 2.0.3
idna 3.4
igraph 0.10.5
importlib-metadata 6.8.0
importlib-resources 6.0.0
ipykernel 6.24.0
ipython 8.12.2
ipython-genutils 0.2.0
ipywidgets 8.0.7
isoduration 20.11.0
iteround 1.0.3
itsdangerous 2.1.2
jedi 0.18.2
Jinja2 3.1.2
joblib 1.3.0
jsonpatch 1.32
jsonpointer 2.0
jsonschema 4.18.0
jsonschema-specifications 2023.6.1
jupyter 1.0.0
jupyter_client 8.3.0
jupyter-console 6.6.3
jupyter_core 5.3.1
jupyter-events 0.6.3
jupyter_server 2.7.0
jupyter_server_terminals 0.4.4
jupyterlab-pygments 0.2.2
jupyterlab-widgets 3.0.8
kiwisolver 1.4.4
libmambapy 0.24.0
llvmlite 0.40.1
logomaker 0.8
loguru 0.7.0
loompy 3.0.7
louvain 0.8.0
lxml 4.9.2
mamba 0.24.0
MarkupSafe 2.1.3
matplotlib 3.6.3
matplotlib-inline 0.1.6
mistune 3.0.1
munkres 1.1.4
mygene 3.2.2
mysql-connector-python 8.0.32
natsort 8.4.0
nbclassic 1.0.0
nbclient 0.8.0
nbconvert 7.6.0
nbformat 5.9.1
nest-asyncio 1.5.6
networkx 3.1
norns 0.1.6
nose 1.3.7
notebook 6.5.4
notebook_shim 0.2.3
numba 0.57.1
numpy 1.22.3
numpy-groupies 0.9.22
openpyxl 3.1.2
overrides 7.3.1
packaging 23.1
palettable 3.3.3
pandas 1.4.2
pandocfilters 1.5.0
parso 0.8.3
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
pip 23.1.2
pkgutil_resolve_name 1.3.10
platformdirs 3.8.1
plotly 5.15.0
pluggy 1.2.0
ply 3.11
pooch 1.7.0
prometheus-client 0.17.1
prompt-toolkit 3.0.39
protobuf 3.20.3
psutil 5.9.5
ptyprocess 0.7.0
pure-eval 0.2.2
pyarrow 9.0.0
pybedtools 0.9.0
pyBigWig 0.3.18
pycosat 0.6.4
pycparser 2.21
pydot 1.4.2
pyfaidx 0.7.2.1
Pygments 2.15.1
PyLD 2.0.3
pynndescent 0.5.10
pyOpenSSL 23.2.0
pyparsing 3.0.9
PyQt5 5.15.7
PyQt5-sip 12.11.0
pysam 0.21.0
PySocks 1.7.1
python-dateutil 2.8.2
python-json-logger 2.0.7
pytz 2023.3
PyVCF3 1.0.3
PyYAML 6.0
pyzmq 25.1.0
qnorm 0.8.1
qtconsole 5.4.3
QtPy 2.3.1
referencing 0.29.1
requests 2.31.0
requests-cache 1.1.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.8.10
ruamel.yaml 0.17.32
ruamel.yaml.clib 0.2.7
scanpy 1.9.3
scikit-learn 1.3.0
scipy 1.10.1
seaborn 0.12.2
Send2Trash 1.8.2
session-info 1.0.0
setuptools 67.8.0
sip 6.7.9
six 1.16.0
sniffio 1.3.0
soupsieve 2.4.1
stack-data 0.6.2
statsmodels 0.14.0
stdlib-list 0.9.0
tenacity 8.2.2
terminado 0.17.1
texttable 1.6.7
threadpoolctl 3.1.0
tinycss2 1.2.1
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
tornado 6.3.2
tqdm 4.65.0
traitlets 5.9.0
typing_extensions 4.7.1
ujson 5.7.0
umap-learn 0.5.3
unicodedata2 15.0.0
uri-template 1.3.0
url-normalize 1.4.3
urllib3 2.0.3
velocyto 0.17.17
wcwidth 0.2.6
webcolors 1.13
webencodings 0.5.1
websocket-client 1.6.1
wheel 0.38.4
widgetsnbextension 4.0.8
xdg 6.0.0
xgboost 1.7.6
XlsxWriter 3.1.2
xxhash 0.0.0
zipp 3.16.0
zstandard 0.19.0
KenjiKamimoto-ac commented
Hi @heroineray , thank you for the feedback!
I guess it may be caused by some incompatibility of celloracle dependent package. I'll look into it and try to solve it.