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GuangyuWangLab2021 / cellDancer

Predict RNA velocity through deep learning
https://guangyuwanglab2021.github.io/cellDancer_website/
BSD 3-Clause "New" or "Revised" License
60 stars 11 forks source link

None of the genes were predicted. #15

Open MSQ-123 opened 1 year ago

MSQ-123 commented 1 year ago

The command I used:

gene_list=['Psd3', 'Dcx', 'Syt11', 'Ntrk2', 'Gnao1', 'Gria1', 'Dctn3', 'Map1b', 'Camk2a', 'Gpm6b', 'Sez6l', 'Evl', 'Astn1', 'Ank2', 'Klf7', 'Tbc1d16', 'Atp1a3', 'Stxbp6', 'Scn2a1', 'Lhx9', 'Slc4a4', 'Ppfia2', 'Kcnip1', 'Ptpro', 'Diaph3', 'Slc1a3', 'Cadm1', 'Mef2c', 'Sptbn1', 'Ncald']

loss_df, cellDancer_df=cd.velocity(cell_type_u_s, gene_list=gene_list, permutation_ratio=0.1, norm_u_s=False, norm_cell_distribution=False, n_jobs=8)

I simply tried to reproduce the DentateGyrus_cell_type analysis, but I encountered this for cd.velocity analysis:

Not predicted gene list:['Kcnip1', 'Map1b', 'Slc1a3', 'Syt11', 'Slc4a4', 'Ptpro', 'Gnao1', 'Gpm6b', 'Klf7', 'Lhx9', 'Tbc1d16', 'Diaph3', 'Ncald', 'Camk2a', 'Scn2a1', 'Psd3', 'Stxbp6', 'Evl', 'Ntrk2', 'Ank2', 'Dctn3', 'Sez6l', 'Atp1a3', 'Cadm1', 'Astn1', 'Ppfia2', 'Sptbn1', 'Gria1', 'Mef2c', 'Dcx']. Try visualizing the unspliced and spliced columns of the gene(s) to check the quality. None of the genes were predicted. Try visualizing the unspliced and spliced columns of the gene(s) to check the quality. @Abclisy. Thanks a lot for your reply

Abclisy commented 1 year ago

Hello, thank you for reaching out. Most of the times when people meet this problem is because of the environment and package versions. The guidance of installation to build a new conda environment with all the fixed version of packages might be helpful. If your problem still exist, could you send us your python version and environment package version list to let us reproduce your problem? Thank you!

MSQ-123 commented 1 year ago

@Abclisy I tried install cellDancer by pip install --no-deps celldancer (Mac M1, python==3.9.16), but I always can not install numpy correctly manually:

Collecting numpy==1.20.3 Using cached numpy-1.20.3.zip (7.8 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Building wheels for collected packages: numpy Building wheel for numpy (pyproject.toml) ... error error: subprocess-exited-with-error

× Building wheel for numpy (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [2271 lines of output] Running from numpy source directory. ########### CLIB COMPILER OPTIMIZATION ########### Platform : Architecture: aarch64 Compiler : clang

  CPU baseline  :
    Requested   : 'min'
    Enabled     : NEON NEON_FP16 NEON_VFPV4 ASIMD
    Flags       : none
    Extra checks: none

  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : ASIMDHP ASIMDDP
    Generated   : none
  CCompilerOpt._cache_write[796] : write cache to path -> /private/var/folders/2j/k27f0c2x3cddhvbwn5_t2x200000gn/T/pip-install-tdmvtdq0/numpy_4b6e851269894e00bbd88b13e4a9526f/build/temp.macosx-11.0-arm64-3.9/ccompiler_opt_cache_clib.py
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for numpy Failed to build numpy ERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projects

or, I have tried python setup.py install, but with cythonize failed:

arning: cython_blas.pyx:1029:46: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.

Error compiling Cython file:

here is my environment:

Name Version Build Channel

absl-py 1.4.0 pypi_0 pypi aiohttp 3.8.5 pypi_0 pypi aiosignal 1.3.1 pypi_0 pypi async-timeout 4.0.3 pypi_0 pypi attrs 23.1.0 pypi_0 pypi bezier 2021.2.12 pypi_0 pypi bzip2 1.0.8 h3422bc3_4 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge ca-certificates 2023.7.22 hf0a4a13_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge cachetools 5.3.1 pypi_0 pypi celldancer 1.1.7 pypi_0 pypi certifi 2023.7.22 pypi_0 pypi charset-normalizer 3.2.0 pypi_0 pypi cython 3.0.0 pypi_0 pypi datashader 0.14.0 pypi_0 pypi filelock 3.12.2 pypi_0 pypi frozenlist 1.4.0 pypi_0 pypi fsspec 2023.6.0 pypi_0 pypi future 0.18.3 pypi_0 pypi google-auth 2.22.0 pypi_0 pypi google-auth-oauthlib 1.0.0 pypi_0 pypi grpcio 1.57.0 pypi_0 pypi idna 3.4 pypi_0 pypi importlib-metadata 6.8.0 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi joblib 1.1.0 pypi_0 pypi jupyterlab 4.0.5 pypi_0 pypi libffi 3.4.2 h3422bc3_5 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge libsqlite 3.42.0 hb31c410_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge libzlib 1.2.13 h53f4e23_5 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge lightning-utilities 0.9.0 pypi_0 pypi markdown 3.4.4 pypi_0 pypi markupsafe 2.1.3 pypi_0 pypi matplotlib 3.5.3 pypi_0 pypi mpmath 1.3.0 pypi_0 pypi multidict 6.0.4 pypi_0 pypi ncurses 6.4 h7ea286d_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge networkx 3.1 pypi_0 pypi numpy 1.25.2 pypi_0 pypi oauthlib 3.2.2 pypi_0 pypi openssl 3.1.2 h53f4e23_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge packaging 23.1 pypi_0 pypi pandas 1.3.4 pypi_0 pypi pip 23.2.1 pyhd8ed1ab_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge protobuf 4.24.1 pypi_0 pypi pyasn1 0.5.0 pypi_0 pypi pyasn1-modules 0.3.0 pypi_0 pypi pybind11 2.11.1 pypi_0 pypi pydeprecate 0.3.1 pypi_0 pypi python 3.9.16 hea58f1e_0_cpython https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge python-dateutil 2.8.2 pypi_0 pypi pytorch-lightning 1.5.2 pypi_0 pypi pytz 2023.3 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi readline 8.2 h92ec313_1 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge requests 2.31.0 pypi_0 pypi requests-oauthlib 1.3.1 pypi_0 pypi rsa 4.9 pypi_0 pypi scikit-image 0.19.2 pypi_0 pypi seaborn 0.11.2 pypi_0 pypi setuptools 59.5.0 pypi_0 pypi setuptools-scm 6.3.2 pypi_0 pypi six 1.16.0 pypi_0 pypi statsmodels 0.13.1 pypi_0 pypi sympy 1.12 pypi_0 pypi tensorboard 2.14.0 pypi_0 pypi tensorboard-data-server 0.7.1 pypi_0 pypi tk 8.6.12 he1e0b03_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge torch 1.10.0 pypi_0 pypi torchmetrics 1.1.0 pypi_0 pypi tqdm 4.66.1 pypi_0 pypi typing-extensions 4.7.1 pypi_0 pypi tzdata 2023c h71feb2d_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge umap-learn 0.5.2 pypi_0 pypi urllib3 1.26.16 pypi_0 pypi werkzeug 2.3.7 pypi_0 pypi wheel 0.41.2 pyhd8ed1ab_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge xz 5.2.6 h57fd34a_0 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge yarl 1.9.2 pypi_0 pypi zipp 3.16.2 pypi_0 pypi

Abclisy commented 1 year ago

Thank you for the information! We will try to reproduce and see what's the reason.