Open aditisk opened 12 months ago
ManuSetty
commented
12 months ago This appears to be an issue with versioning of different python modules. Can you please try again with a new conda environment? We also suggest using a python version > 3.8
aditisk
commented
12 months ago Thanks for the suggestions. I tried using v3.9 and v3.10 in a virtual environment but now I am unable to run PCA (and all steps after that) on my adata object.
`--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[10], line 2 1 # Note in the manuscript, we did not use highly variable genes but scanpy by default uses only highly variable genes ----> 2 sc.tl.pca(adata)
File ~/.local/lib/python3.10/site-packages/scanpy/preprocessing/_pca.py:200, in pca(data, n_comps, zero_center, svd_solver, random_state, return_info, use_highly_variable, dtype, copy, chunked, chunk_size) 194 if svd_solver not in {'lobpcg', 'arpack'}: 195 raise ValueError( 196 'svd_solver: {svd_solver} can not be used with sparse input.\n' 197 'Use "arpack" (the default) or "lobpcg" instead.' 198 ) --> 200 output = _pca_with_sparse( 201 X, n_comps, solver=svd_solver, random_state=random_state 202 ) 203 # this is just a wrapper for the results 204 X_pca = output['X_pca']
File ~/.local/lib/python3.10/site-packages/scanpy/preprocessing/_pca.py:303, in _pca_with_sparse(X, npcs, solver, mu, random_state) 292 return XHmat(x) - mhmat(ones(x)) 294 XL = LinearOperator( 295 matvec=matvec, 296 dtype=X.dtype, (...) 300 rmatmat=rmatmat, 301 ) --> 303 u, s, v = svds(XL, solver=solver, k=npcs, v0=random_init) 304 u, v = svd_flip(u, v) 305 idx = np.argsort(-s)
File ~/.local/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/_svds.py:443, in svds(A, k, ncv, tol, which, v0, maxiter, return_singular_vectors, solver, random_state, options) 104 def svds(A, k=6, ncv=None, tol=0, which='LM', v0=None, 105 maxiter=None, return_singular_vectors=True, 106 solver='arpack', random_state=None, options=None): 107 """ 108 Partial singular value decomposition of a sparse matrix. 109 (...) 441 442 """ --> 443 args = _iv(A, k, ncv, tol, which, v0, maxiter, return_singular_vectors, 444 solver, random_state) 445 (A, k, ncv, tol, which, v0, maxiter, 446 return_singular_vectors, solver, random_state) = args 448 largest = (which == 'LM')
File ~/.local/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/_svds.py:40, in _iv(A, k, ncv, tol, which, v0, maxiter, return_singular, solver, random_state)
37 if not (np.issubdtype(A.dtype, np.complexfloating)
38 or np.issubdtype(A.dtype, np.floating)):
39 message = "A must be of floating or complex floating data type."
---> 40 raise ValueError(message)
41 if np.prod(A.shape) == 0:
42 message = "A must not be empty."
ValueError: A must be of floating or complex floating data type.`
Hello,
I am trying to run Palantir on my dataset to be able to eventually use Cellrank2. I am getting an error message (pasted below). I have loaded the scipy module and imported the necessary features as mentioned in the tutorial. How can I fix this? Thanks.
`--------------------------------------------------------------------------- _RemoteTraceback Traceback (most recent call last) _RemoteTraceback: """ Traceback (most recent call last): File "/ihome/crc/install/python/ondemand-jupyter-python3.8/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 616, in wait_result_broken_or_wakeup result_item = result_reader.recv() File "/ihome/crc/install/python/ondemand-jupyter-python3.8/lib/python3.8/multiprocessing/connection.py", line 251, in recv return _ForkingPickler.loads(buf.getbuffer()) ModuleNotFoundError: No module named 'scipy.sparse._csr' """
The above exception was the direct cause of the following exception:
BrokenProcessPool Traceback (most recent call last)