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inhomogeneous shape when running TFvelo_analysis_demo.py #19

@ogandril

Description

@ogandril

When I try to analyse the output on the given example

python TFvelo_analysis_demo.py --dataset_name pancreas

I get the following error:
(TFVelo_venv) [ogandril@cca015 ~/TFvelo]$ python TFvelo_analysis_demo.py --dataset_name pancreas

Namespace(dataset_name='pancreas', layer='M_total', basis='umap', loss_percent_thres=50, spearmanr_thres=0.8, save_name='_demo', data_path='TFvelo_pancreas_demo/')
Checking highly_variable_genes
AnnData object with n_obs × n_vars = 3696 × 2000
obs: 'clusters_coarse', 'clusters', 'S_score', 'G2M_score', 'n_genes', 'initial_size_spliced', 'initial_size_unspliced', 'initial_size_total', 'initial_size', 'n_counts'
var: 'highly_variable_genes', 'n_cells', 'gene_count_corr', 'means', 'dispersions', 'dispersions_norm', 'highly_variable', 'n_TFs', 'fit_alpha', 'fit_beta', 'fit_omega', 'fit_theta', 'fit_gamma', 'fit_delta', 'fit_likelihood', 'fit_varx', 'fit_scaling_y'
uns: 'all_TFs', 'clusters_coarse_colors', 'clusters_colors', 'day_colors', 'genes_all', 'genes_pp', 'neighbors', 'pca', 'recover_dynamics'
obsm: 'X_pca', 'X_umap'
varm: 'TFs', 'TFs_correlation', 'TFs_id', 'TFs_times', 'fit_scaling', 'fit_weights', 'fit_weights_final', 'fit_weights_init', 'knockTF_Log2FC', 'loss'
layers: 'M_total', 'WX', 'filtered', 'fit_t', 'fit_t_raw', 'spliced', 'total', 'total_raw', 'unspliced', 'velo_hat', 'velo_normed', 'velo_t', 'y', 'y_t'
obsp: 'connectivities', 'distances'
computing velocity graph (using 1/32 cores)
WARNING: Unable to create progress bar. Consider installing tqdm as pip install tqdm and ipywidgets as pip install ipywidgets,
or disable the progress bar using show_progress_bar=False.
Traceback (most recent call last):
File "/pbs/home/o/ogandril/TFvelo/TFvelo_analysis_demo.py", line 202, in
main(args)
File "/pbs/home/o/ogandril/TFvelo/TFvelo_analysis_demo.py", line 151, in main
adata = get_pseudotime(adata)
File "/pbs/home/o/ogandril/TFvelo/TFvelo_analysis_demo.py", line 36, in get_pseudotime
TFv.tl.velocity_graph(adata, basis=None, vkey='velocity', xkey='M_total')
File "/pbs/home/o/ogandril/TFvelo/TFvelo/tools/velocity_graph.py", line 360, in velocity_graph
vgraph.compute_cosines(n_jobs=n_jobs, backend=backend)
File "/pbs/home/o/ogandril/TFvelo/TFvelo/tools/velocity_graph.py", line 174, in compute_cosines
res = parallelize(
File "/pbs/home/o/ogandril/TFvelo/TFvelo/core/_parallelize.py", line 138, in wrapper
res = np.array(res) if as_array else res
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (1, 4) + inhomogeneous part.
Traceback (most recent call last):
File "/usr/lib64/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/lib64/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib64/python3.9/multiprocessing/managers.py", line 591, in _run_server
server.serve_forever()
File "/usr/lib64/python3.9/multiprocessing/managers.py", line 184, in serve_forever
sys.exit(0)
SystemExit: 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/lib64/python3.9/multiprocessing/util.py", line 300, in _run_finalizers
finalizer()
File "/usr/lib64/python3.9/multiprocessing/util.py", line 224, in call
res = self._callback(*self._args, **self._kwargs)
File "/usr/lib64/python3.9/multiprocessing/util.py", line 133, in _remove_temp_dir
rmtree(tempdir)
File "/usr/lib64/python3.9/shutil.py", line 734, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/usr/lib64/python3.9/shutil.py", line 690, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File "/usr/lib64/python3.9/shutil.py", line 688, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
OSError: [Errno 16] Device or resource busy: '.nfs00000001dc551e61000092e3'

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