Error in protein module computation
Hello!
I have looked through the issues and couldn’t find the error I am currently encountering. I’m using vContact2 version 0.11.3.
Here’s the error:
INFO:vcontact2.modules: Loading the clustering results
ERROR:vcontact2: Error in protein module computation
ERROR:vcontact2: Inexact indices into sparse matrices are not allowed
Traceback (most recent call last):
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/scipy/sparse/_sputils.py", line 208, in isintlike
operator.index(x)
TypeError: 'float' object cannot be interpreted as an integer
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/modules/bin/vcontact/0.11.3/bin/vcontact2", line 724, in main
modules = vcontact2.modules.Modules(pcp, output_dir, threshold=args.mod_sig, inflation=args.mod_inflation,
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/vcontact2/modules.py", line 65, in init
self.matrix_module = self.module_in_contigs() # Calls self.matrix, returns matrix w/ proportion of module's PCs in contig
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/vcontact2/modules.py", line 198, in module_in_contigs
N[:, m] = matrix[:, pos].sum(1)
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/scipy/sparse/_lil.py", line 332, in setitem
IndexMixin.setitem(self, key, x)
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/scipy/sparse/_index.py", line 97, in setitem
row, col = self._validate_indices(key)
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/scipy/sparse/_index.py", line 161, in _validate_indices
if isintlike(col):
File "/mnt/modules/bin/vcontact/0.11.3/lib/python3.9/site-packages/scipy/sparse/_sputils.py", line 216, in isintlike
raise ValueError(msg)
ValueError: Inexact indices into sparse matrices are not allowed
WRT outputs, I think I am seeing every expected file except for the genome-by-genome overview.
I’ve tried running vContact2 using my own data and the test data included in this repository and get the same result.
Thank you.
Comments (3)
-
reporter -
reporter The same question was asked and addressed a couple days after I posted here: https://bitbucket.org/MAVERICLab/vcontact2/issues/84/vcontact2-error-in-protein-module
Changing the scipy version to 1.6.0 and then reinstalling vcontact2 via conda allowed vcontact2 version 11.3 to work for me.
-
reporter - changed status to resolved
See final comment.
- Log in to comment
I will add that this was installed using conda, if that helps track down the issue.