None of the genes were predicted. #15

MSQ-123 · 2023-08-23T12:08:44Z

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 · 2023-08-23T13:46:04Z

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 · 2023-08-23T14:38:14Z

@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:

Abclisy · 2023-08-24T19:21:33Z

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

stemjn mentioned this issue Jan 6, 2024

torch version compatibility #23

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None of the genes were predicted. #15

None of the genes were predicted. #15

MSQ-123 commented Aug 23, 2023 •

edited

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Abclisy commented Aug 23, 2023

MSQ-123 commented Aug 23, 2023

Abclisy commented Aug 24, 2023

None of the genes were predicted. #15

None of the genes were predicted. #15

Comments

MSQ-123 commented Aug 23, 2023 • edited Loading

Abclisy commented Aug 23, 2023

MSQ-123 commented Aug 23, 2023

@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:

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:

Error compiling Cython file:

Name Version Build Channel

Abclisy commented Aug 24, 2023

MSQ-123 commented Aug 23, 2023 •

edited

Loading

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