Open danli349 opened 1 year ago
Hello:
Can you please let me know what is the reason of this error? Thanks
clf = doubletdetection.BoostClassifier( n_iters=10, clustering_algorithm="louvain", standard_scaling=True, pseudocount=0.1, n_jobs=-1, ) doublets = clf.fit(adata.X).predict(p_thresh=1e-16, voter_thresh=0.5) doublet_score = clf.doublet_score()
Exception ignored on calling ctypes callback function: <function _ThreadpoolInfo._find_modules_with_dl_iterate_phdr.<locals>.match_module_callback at 0x7f1efcee03a0> Traceback (most recent call last): File "/home/dan/miniconda3/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback self._make_module_from_path(filepath) File "/home/dan/miniconda3/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path module = module_class(filepath, prefix, user_api, internal_api) File "/home/dan/miniconda3/lib/python3.8/site-packages/threadpoolctl.py", line 606, in __init__ self.version = self.get_version() File "/home/dan/miniconda3/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version config = get_config().split() AttributeError: 'NoneType' object has no attribute 'split' --------------------------------------------------------------------------- IndexError Traceback (most recent call last) Cell In[8], line 1 ----> 1 doublets = clf.fit(adata.X).predict(p_thresh=1e-16, voter_thresh=0.5) 2 doublet_score = clf.doublet_score() File ~/miniconda3/lib/python3.8/site-packages/doubletdetection/doubletdetection.py:208, in BoostClassifier.fit(self, raw_counts) 206 if self.verbose: 207 print("Iteration {:3}/{}".format(i + 1, self.n_iters)) --> 208 self.all_scores_[i], self.all_log_p_values_[i] = self._one_fit() 209 all_communities[i] = self.communities_ 210 all_parents.append(self.parents_) File ~/miniconda3/lib/python3.8/site-packages/doubletdetection/doubletdetection.py:333, in BoostClassifier._one_fit(self) 331 f = io.StringIO() 332 with redirect_stdout(f): --> 333 fullcommunities, _, _ = phenograph.cluster( 334 aug_counts.obsm["X_pca"], n_jobs=self.n_jobs, **self.clustering_kwargs 335 ) 336 out = f.getvalue() 337 if self.verbose: File ~/miniconda3/lib/python3.8/site-packages/phenograph/cluster.py:350, in cluster(data, clustering_algo, k, directed, prune, min_cluster_size, jaccard, primary_metric, n_jobs, q_tol, louvain_time_limit, nn_method, partition_type, resolution_parameter, n_iterations, use_weights, seed, **kargs) 348 communities, Q = "", "" 349 if clustering_algo == "louvain": --> 350 communities, Q = run_louvain(graph, q_tol, louvain_time_limit) 352 elif clustering_algo == "leiden": 353 communities, Q = run_leiden( 354 graph, 355 directed, (...) 361 kargs, 362 ) File ~/miniconda3/lib/python3.8/site-packages/phenograph/cluster.py:164, in run_louvain(graph, q_tol, louvain_time_limit) 162 uid = uuid.uuid1().hex 163 graph2binary(uid, graph) --> 164 communities, Q = runlouvain(uid, tol=q_tol, time_limit=louvain_time_limit) 166 # clean up 167 for f in os.listdir(): File ~/miniconda3/lib/python3.8/site-packages/phenograph/core.py:293, in runlouvain(filename, max_runs, time_limit, tol) 290 run += 1 292 # continue only if we've reached a higher modularity than before --> 293 if q[-1] - Q > tol: 295 Q = q[-1] 296 updated = run IndexError: list index out of range
Hello:
Can you please let me know what is the reason of this error? Thanks