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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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scv.vl.velocity_graph won't finish after hours with 0 #1196

Closed didiren closed 6 months ago

didiren commented 6 months ago

...

# paste your code here, if applicable
Error output ```pytb # paste the error output here, if applicable ```
Versions ```pytb # paste the ouput of scv.logging.print_versions() here ```
didiren commented 6 months ago

Hi, After following the tutorial of using scvelo, all steps ran fine but stuck when running scv.tl.velocity_graph. The run didn't show any error but took long hours without any progress.

Would you please comment on what I should do to successfully run it?

My packages list are here: Package Version

absl-py 2.1.0 anndata 0.9.2 anyio 4.2.0 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 arrow 1.3.0 asttokens 2.4.1 async-lru 2.0.4 attrs 23.2.0 Babel 2.14.0 backcall 0.2.0 beautifulsoup4 4.12.3 bleach 6.1.0 certifi 2024.2.2 cffi 1.16.0 charset-normalizer 3.3.2 click 8.1.7 colorama 0.4.6 comm 0.2.1 contourpy 1.1.1 cycler 0.12.1 debugpy 1.8.1 decorator 5.1.1 defusedxml 0.7.1 exceptiongroup 1.2.0 executing 2.0.1 fastjsonschema 2.19.1 flatbuffers 2.0.7 fonttools 4.48.1 fqdn 1.5.1 get-annotations 0.1.2 gitdb 4.0.11 GitPython 3.1.41 h5py 3.10.0 idna 3.6 igraph 0.10.8 importlib-metadata 7.0.1 importlib-resources 6.1.1 ipykernel 6.29.2 ipython 8.12.3 ipython-genutils 0.2.0 ipywidgets 7.7.1 isoduration 20.11.0 jax 0.3.13 jaxlib 0.3.7 jedi 0.19.1 Jinja2 3.1.3 joblib 1.3.2 json5 0.9.14 jsonpointer 2.4 jsonschema 4.21.1 jsonschema-specifications 2023.12.1 jupyter_client 8.6.0 jupyter_core 5.7.1 jupyter-events 0.9.0 jupyter-lsp 2.2.2 jupyter_server 2.12.5 jupyter_server_terminals 0.5.2 jupyterlab 4.0.12 jupyterlab_pygments 0.3.0 jupyterlab_server 2.25.2 jupyterlab_widgets 3.0.10 kiwisolver 1.4.5 llvmlite 0.41.1 loompy 3.0.7 louvain 0.8.1 MarkupSafe 2.1.5 matplotlib 3.7.4 matplotlib-inline 0.1.6 mistune 3.0.2 multivelo 0.1.3 natsort 8.4.0 nbclient 0.9.0 nbconvert 7.16.0 nbformat 5.9.2 nest-asyncio 1.6.0 networkx 3.1 notebook 7.0.8 notebook_shim 0.2.3 numba 0.58.1 numpy 1.24.4 numpy_groupies 0.9.22 opt-einsum 3.3.0 overrides 7.7.0 packaging 23.2 pandas 2.0.3 pandocfilters 1.5.1 parso 0.8.3 patsy 0.5.6 pickleshare 0.7.5 pillow 10.2.0 pip 24.0 pkgutil_resolve_name 1.3.10 platformdirs 4.2.0 prometheus-client 0.19.0 prompt-toolkit 3.0.43 psutil 5.9.8 pure-eval 0.2.2 pycparser 2.21 Pygments 2.17.2 pynndescent 0.5.11 pyparsing 3.1.1 python-dateutil 2.8.2 python-json-logger 2.0.7 pytz 2024.1 pywin32 306 pywinpty 2.0.12 PyYAML 6.0.1 pyzmq 25.1.2 referencing 0.33.0 requests 2.31.0 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rpds-py 0.17.1 scanpy 1.9.8 scikit-learn 1.1.3 scipy 1.10.1 scvelo 0.3.1 seaborn 0.13.2 Send2Trash 1.8.2 session-info 1.0.0 setuptools 49.2.1 six 1.16.0 smmap 5.0.1 sniffio 1.3.0 soupsieve 2.5 stack-data 0.6.3 statsmodels 0.14.1 stdlib-list 0.10.0 terminado 0.18.0 texttable 1.7.0 threadpoolctl 3.2.0 tinycss2 1.2.1 tomli 2.0.1 tornado 6.4 tqdm 4.66.2 traitlets 5.14.1 types-python-dateutil 2.8.19.20240106 typing_extensions 4.9.0 tzdata 2024.1 umap-learn 0.5.5 uri-template 1.3.0 urllib3 2.2.0 wcwidth 0.2.13 webcolors 1.13 webencodings 0.5.1 websocket-client 1.7.0 widgetsnbextension 3.6.6 zipp 3.17.0

WeilerP commented 6 months ago

Since there is no stack trace or anything to work with, I cannot help you here, unfortunately. Everything works fine on my end.