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.

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