vcontact2: Error in protein module computation
Issue #84
new
Hi, I ran the following and obtained the error: vcontact2: Error in protein module computation.
vcontact2 --raw-proteins filtered_phages_clean.faa --proteins-fp phages_genomes_g2g.csv --db 'ProkaryoticViralRefSeq211-Merged' --pcs-mode MCL --vcs-mode ClusterONE --c1-bin conda/envs/vContact2/bin/cluster_one-1.0.jar --output-dir /vcontact2_silage -t 14
I look around in the issues but I could not find anything similar previously report. I also recently re install the tool using conda.
can someone please point to me what I am doing wrong?
?[1;42mINFO?[1;0m:vcontact2.modules: Loading the clustering results
?[1;41mERROR?[1;0m:vcontact2: Error in protein module computation
?[1;41mERROR?[1;0m:vcontact2: Inexact indices into sparse matrices are not allowed
Traceback (most recent call last):
File "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/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 "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/bin/vcontact2", line 724, in main
modules = vcontact2.modules.Modules(pcp, output_dir, threshold=args.mod_sig, inflation=args.mod_inflation,
File "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/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 "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/site-packages/vcontact2/modules.py", line 198, in module_in_contigs
N[:, m] = matrix[:, pos].sum(1)
File "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/site-packages/scipy/sparse/_lil.py", line 332, in __setitem__
IndexMixin.__setitem__(self, key, x)
File "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/site-packages/scipy/sparse/_index.py", line 97, in __setitem__
row, col = self._validate_indices(key)
File "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/site-packages/scipy/sparse/_index.py", line 161, in _validate_indices
if isintlike(col):
File "/beegfs/work/workspace/ws/ho_kezau83-conda-0/conda/envs/vContact2/lib/python3.10/site-packages/scipy/sparse/_sputils.py", line 216, in isintlike
raise ValueError(msg)
ValueError: Inexact indices into sparse matrices are not allowed
Thank you for your help.
Best,
Johan Sebastián
Comments (5)
-
-
I tried to reinstall
scipyto 1.6.0 on my MacBook. It seems work. -
Hi there,
I’m also having this problem :(
I reinstalled scipy to 1.6.0 but still no luck. Anything else it could be?
Thanks,
Cassie
-
Okay update for me as well (for anyone that may also be struggling like I was) - I had to revert my python back to v2.9 (I was using the newest) and then I could revert to scipy 1.6.0 and it worked for me! woohoo
-
Hi Cassie S，I met the same problem with you. Will python v2.9 makes mistake? The author said python >=3.7
- Log in to comment
I met the same problem as Johan's.
I checked all the dependencies, and they are subject to the demands.
Conda list:
Here’s my command:
No generic_by_genome_overview.csv generated.
It seems it’s the problem with the package,
scipy. But I have no idea what’s going on.
Looking for help. Thanks in advance!
Greets,
Mei