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dimension_reduction failed for method='se' #148

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xyang2uchicago opened this issue May 9, 2024 · 0 comments
Open

dimension_reduction failed for method='se' #148

xyang2uchicago opened this issue May 9, 2024 · 0 comments

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@xyang2uchicago
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xyang2uchicago commented May 9, 2024

Hi, I am running dimension_reduction function for my 200k+ cells.
It works well when I call

st.dimension_reduction(adata, method='pca', n_neighbors=n_neighbors, feature='top_pcs', n_components=5, n_jobs=32)

However, it takes a while and was killed when I didn't specify the method, thus using default method='se':

st.dimension_reduction(adata, n_neighbors=n_neighbors, feature='top_pcs', n_components=5, n_jobs=32)

There is error I don't know how to debug:
Can't expand MemType 3: jcol 160965
Traceback (most recent call last):
File "", line 1, in
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/stream/core.py", line 1179, in dimension_reduction
trans = reducer.fit(input_data)
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/sklearn/manifold/_spectral_embedding.py", line 651, in fit
random_state=random_state,
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/sklearn/manifold/_spectral_embedding.py", line 300, in spectral_embedding
laplacian, k=n_components, sigma=1.0, which="LM", tol=eigen_tol, v0=v0
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 1645, in eigsh
hermitian=True, tol=tol)
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 1073, in get_OPinv_matvec
return SpLuInv(A).matvec
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 913, in init
self.M_lu = splu(M)
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/scipy/sparse/linalg/dsolve/linsolve.py", line 339, in splu
ilu=False, options=_options)
SystemError: gstrf was called with invalid arguments

Anyone can help? Thank you.

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