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DongqingSun96 / STRIDE

STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using single-cell transcriptomics data.

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IndexError: cannot do a non-empty take from an empty axes.

juliaryann opened this issue · comments

commented

Hello! Thank you for making this package! I got this error and I'm not sure what it means.

STRIDE deconvolve --sc-count /home/salatti/Desktop/sc_count.csv --sc-celltype /home/salatti/Desktop/sc_meta.csv --st-count /home/salatti/Desktop/spatial_count.csv --outdir /home/salatti/Desktop --outprefix stride_deconv --normalize
Reading spatial count matrix...
Traceback (most recent call last):
 File "/home/salatti/anaconda3/envs/stride/bin/STRIDE", line 4, in <module>
   __import__('pkg_resources').run_script('stridespatial==0.0.2a0', 'STRIDE')
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/pkg_resources/__init__.py", line 662, in run_script
   self.require(requires)[0].run_script(script_name, ns)
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1466, in run_script
   exec(script_code, namespace, namespace)
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/stridespatial-0.0.2a0-py3.8.egg/EGG-INFO/scripts/STRIDE", line 72, in <module>
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/stridespatial-0.0.2a0-py3.8.egg/EGG-INFO/scripts/STRIDE", line 45, in main
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/stridespatial-0.0.2a0-py3.8.egg/STRIDE/Deconvolution.py", line 218, in Deconvolve
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/stridespatial-0.0.2a0-py3.8.egg/STRIDE/ModelTrain.py", line 94, in stProcess
 File "<__array_function__ internals>", line 180, in quantile
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4371, in quantile
   return _quantile_unchecked(
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4383, in _quantile_unchecked
   r, k = _ureduce(a,
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3702, in _ureduce
   r = func(a, **kwargs)
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4552, in _quantile_ureduce_func
   result = _quantile(arr,
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4658, in _quantile
   take(arr, indices=-1, axis=DATA_AXIS)
 File "<__array_function__ internals>", line 180, in take
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 190, in take
   return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
 File "/home/salatti/anaconda3/envs/stride/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
   return bound(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.

Thank you for your assistance,
Julia

commented

Hi, could you please provide the input files for debugging? Thanks!