I ran Cogent at the beginning of this year with no issue.
I recently have recreated the environment and tried to use it and am having issues with the process_kmer_to_graph.py step.
When I run it this is the error I get:
File "/home/khnfar025/.conda/envs/anaCogent/lib/python3.7/site-packages/networkx-2.7.1-py3.7.egg/networkx/convert_matrix.py", line 1020, in to_scipy_sparse_matrix
G, nodelist=nodelist, dtype=dtype, weight=weight, format=format
File "/home/khnfar025/.conda/envs/anaCogent/lib/python3.7/site-packages/networkx-2.7.1-py3.7.egg/networkx/convert_matrix.py", line 921, in to_scipy_sparse_array
A = sp.sparse.coo_array((d, (r, c)), shape=(nlen, nlen), dtype=dtype)
AttributeError: module 'scipy.sparse' has no attribute 'coo_array'
To me it sounds like scipy version 1.8.0 is required for coo_array. Conda install currently only install version 1.7.3.
Is this something that can be fixed on your side in the install instructions? I have had difficulty having this resolved by the sys admin for the hpc that I use at my institution.
Hi Magdoll,
I ran Cogent at the beginning of this year with no issue.
I recently have recreated the environment and tried to use it and am having issues with the process_kmer_to_graph.py step.
When I run it this is the error I get:
File "/home/khnfar025/.conda/envs/anaCogent/lib/python3.7/site-packages/networkx-2.7.1-py3.7.egg/networkx/convert_matrix.py", line 1020, in to_scipy_sparse_matrix G, nodelist=nodelist, dtype=dtype, weight=weight, format=format File "/home/khnfar025/.conda/envs/anaCogent/lib/python3.7/site-packages/networkx-2.7.1-py3.7.egg/networkx/convert_matrix.py", line 921, in to_scipy_sparse_array A = sp.sparse.coo_array((d, (r, c)), shape=(nlen, nlen), dtype=dtype) AttributeError: module 'scipy.sparse' has no attribute 'coo_array'
This is the resource that I've found on the issue : https://github.com/pyg-team/pytorch_geometric/issues/4378
To me it sounds like scipy version 1.8.0 is required for coo_array. Conda install currently only install version 1.7.3.
Is this something that can be fixed on your side in the install instructions? I have had difficulty having this resolved by the sys admin for the hpc that I use at my institution.
thanks for your consideration, Farrah Khan