cnv.tl.infercnv error
Dacy34 opened this issue · comments
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Dear infercny team.
Thanks for bringing infercnv to python.I had a strange error using infercnvpy.That is, when you run cnv.tl.infercnv, after a few minutes of processing, the function will simply stop running but still shown running.When you look at the task in the background, you'll see that python's cpu usage is 0 and memory remains static.The bug appeared when using both its own data and infercnvpy's own data.I created this bug in both the SCVI environment and the dedicated infercnv environment.How can I solve this bug?
Looking forward to your reply, thank you
Version information
SCVI environment :
session_info 1.0.0
-----
anyio NA
arrow 1.2.3
asttokens NA
attr 22.2.0
babel 2.11.0
backcall 0.2.0
certifi 2022.12.07
charset_normalizer 2.1.1
colorama 0.4.6
comm 0.1.2
cython_runtime NA
dateutil 2.8.2
debugpy 1.6.6
decorator 5.1.1
executing 1.2.0
fastjsonschema NA
fqdn NA
google NA
idna 3.4
importlib_metadata NA
importlib_resources NA
ipykernel 6.21.1
ipython_genutils 0.2.0
isoduration NA
jedi 0.18.2
jinja2 3.1.2
json5 NA
jsonpointer 2.3
jsonschema 4.17.3
jupyter_events 0.5.0
jupyter_server 2.2.1
jupyterlab_server 2.19.0
markupsafe 2.1.2
mpl_toolkits NA
nbformat 5.7.3
nt NA
ntsecuritycon NA
packaging 23.0
parso 0.8.3
pickleshare 0.7.5
pkg_resources NA
platformdirs 2.6.2
prometheus_client NA
prompt_toolkit 3.0.36
psutil 5.9.4
pure_eval 0.2.2
pvectorc NA
pydev_ipython NA
pydevconsole NA
pydevd 2.9.5
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.14.0
pyrsistent NA
pythoncom NA
pythonjsonlogger NA
pywin32_bootstrap NA
pywin32_system32 NA
pywintypes NA
requests 2.28.2
rfc3339_validator 0.1.4
rfc3986_validator 0.1.1
send2trash NA
six 1.16.0
sniffio 1.3.0
stack_data 0.6.2
tornado 6.2
traitlets 5.9.0
uri_template NA
urllib3 1.26.14
wcwidth 0.2.6
webcolors 1.11.1
websocket 1.5.1
win32api NA
win32com NA
win32con NA
win32security NA
win32trace NA
winerror NA
yaml 5.4.1
zipp NA
zmq 25.0.0
-----
IPython 8.9.0
jupyter_client 8.0.2
jupyter_core 5.2.0
jupyterlab 3.6.1
notebook 6.5.2
-----
Python 3.8.16 | packaged by conda-forge | (default, Feb 1 2023, 15:53:35) [MSC v.1929 64 bit (AMD64)]
Windows-10-10.0.19044-SP0
-----
Session information updated at 2023-02-07 18:24
infercnv environment:
anndata 0.8.0
infercnvpy 0.4.1
matplotlib 3.6.3
numpy 1.23.5
pandas 1.5.3
scanpy 1.9.1
scipy 1.10.0
session_info 1.0.0
-----
PIL 9.4.0
asttokens NA
backcall 0.2.0
cairo 1.23.0
colorama 0.4.6
comm 0.1.2
cycler 0.10.0
cython_runtime NA
dateutil 2.8.2
debugpy 1.6.6
decorator 5.1.1
executing 1.2.0
gtfparse NA
h5py 3.8.0
igraph 0.10.4
importlib_metadata NA
ipykernel 6.21.1
ipywidgets 8.0.4
jedi 0.18.2
joblib 1.2.0
kiwisolver 1.4.4
leidenalg 0.9.1
llvmlite 0.39.1
mpl_toolkits NA
natsort 8.2.0
nt NA
ntsecuritycon NA
numba 0.56.4
packaging 23.0
parso 0.8.3
pickleshare 0.7.5
pkg_resources NA
platformdirs 3.0.0
polars 0.16.2
prompt_toolkit 3.0.36
psutil 5.9.4
pure_eval 0.2.2
pydev_ipython NA
pydevconsole NA
pydevd 2.9.5
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.14.0
pyparsing 3.0.9
pyreadr 0.4.7
pythoncom NA
pytz 2022.7.1
pywin32_bootstrap NA
pywin32_system32 NA
pywintypes NA
setuptools 67.1.0
six 1.16.0
sklearn 1.2.1
stack_data 0.6.2
texttable 1.6.7
threadpoolctl 3.1.0
tornado 6.2
tqdm 4.64.1
traitlets 5.9.0
typing_extensions NA
wcwidth 0.2.6
win32api NA
win32com NA
win32security NA
zipp NA
zmq 25.0.0
zoneinfo NA
-----
IPython 8.9.0
jupyter_client 8.0.2
jupyter_core 5.2.0
-----
Python 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:28:38) [MSC v.1929 64 bit (AMD64)]
Windows-10-10.0.19044-SP0
-----
Session information updated at 2023-02-07 18:22
Hi @Dacy34,
this is indeed weird. My first suspicion would be that this is related to multi-threading. Could you try running tl.infercnv with n_jobs=1?
Hi @grst,
thanks for your advice! I have tried tl.infercnv with n_jobs=1 and n_jobs=8. It comes to the same result, stop running but still shown running with cpu usage 0. This error comes after I created the SCVI conda envrioment with GPU avaliable, as shown in my first time report. Before I create this envrioment, I also run the infercnvpy correctly once. But that conda enviroment have already been removed. And even I created the infercnv environment still can't solve this error, that's really pullze me.
