ValueError: need at least one array to concatenate
Bio-MingChen opened this issue · comments
I encountered an error show below when running cnv.tl.infercnv(), the h5ad file I used is also uploaded ,do you have any suggestions?
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_RemoteTraceback Traceback (most recent call last)
_RemoteTraceback:
"""
Traceback (most recent call last):
File "c:\users\lenovo\appdata\local\programs\python\python38\lib\concurrent\futures\process.py", line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "c:\users\lenovo\appdata\local\programs\python\python38\lib\concurrent\futures\process.py", line 198, in _process_chunk
return [fn(*args) for args in chunk]
File "c:\users\lenovo\appdata\local\programs\python\python38\lib\concurrent\futures\process.py", line 198, in <listcomp>
return [fn(*args) for args in chunk]
File "c:\users\lenovo\appdata\local\programs\python\python38\lib\site-packages\infercnvpy\tl\_infercnv.py", line 353, in _infercnv_chunk
chr_pos, x_smoothed = _running_mean_by_chromosome(
File "c:\users\lenovo\appdata\local\programs\python\python38\lib\site-packages\infercnvpy\tl\_infercnv.py", line 273, in _running_mean_by_chromosome
return chr_start_pos, np.hstack(running_means)
File "<__array_function__ internals>", line 5, in hstack
File "c:\users\lenovo\appdata\local\programs\python\python38\lib\site-packages\numpy\core\shape_base.py", line 346, in hstack
return _nx.concatenate(arrs, 1)
File "<__array_function__ internals>", line 5, in concatenate
ValueError: need at least one array to concatenate
The code I used is
ecc7 = sc.read('data/ecc7_add_gtf.h5ad')
sc.tl.pca(ecc7)
sc.pp.neighbors(ecc7)
sc.tl.louvain(ecc7)
cnv.tl.infercnv(ecc7,reference_key='louvain')
In fact,infercnv requires chromosome startswith 'chr' and range from chr1 to chr22 other sequences will be ignored, so, that's the point, what I need is to add chr to chromosome.