Traceback (most recent call last):
File "/usr/local/bin/scanpy-multiplet", line 10, in <module>
sys.exit(multiplet())
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/scanpy_scripts/cmd_utils.py", line 46, in cmd
func(adata, **kwargs)
File "/usr/local/lib/python3.9/site-packages/scanpy_scripts/lib/_scrublet.py", line 24, in scrublet
sce.pp.scrublet(adata, adata_sim=adata_sim, **kwargs)
File "/usr/local/lib/python3.9/site-packages/scanpy/external/pp/_scrublet.py", line 239, in scrublet
scrubbed = [
File "/usr/local/lib/python3.9/site-packages/scanpy/external/pp/_scrublet.py", line 240, in <listcomp>
_run_scrublet(
File "/usr/local/lib/python3.9/site-packages/scanpy/external/pp/_scrublet.py", line 210, in _run_scrublet
ad_obs = _scrublet_call_doublets(
File "/usr/local/lib/python3.9/site-packages/scanpy/external/pp/_scrublet.py", line 434, in _scrublet_call_doublets
sl.pipeline_pca(
File "/usr/local/lib/python3.9/site-packages/scrublet/helper_functions.py", line 91, in pipeline_pca
pca = PCA(n_components=n_prin_comps, random_state=random_state, svd_solver=svd_solver).fit(X_obs)
File "/usr/local/lib/python3.9/site-packages/sklearn/decomposition/_pca.py", line 382, in fit
self._fit(X)
File "/usr/local/lib/python3.9/site-packages/sklearn/decomposition/_pca.py", line 459, in _fit
return self._fit_truncated(X, n_components, self._fit_svd_solver)
File "/usr/local/lib/python3.9/site-packages/sklearn/decomposition/_pca.py", line 543, in _fit_truncated
raise ValueError(
ValueError: n_components=30 must be between 1 and min(n_samples, n_features)=21 with svd_solver='arpack'
We should have some logic that either filters out samples with less than 30 cells before running scrubblet or something that allow the user to indicate that this should fail like this if getting to this point.
I guess this is not unexpected:
We should have some logic that either filters out samples with less than 30 cells before running scrubblet or something that allow the user to indicate that this should fail like this if getting to this point.