AttributeError: module 'numpy' has no attribute 'warnings'

[Former user]

Hello,

I installed vContact2 via the conda installation. I am getting the following error:

AttributeError: module 'numpy' has no attribute 'warnings'. Did you mean: 'hanning'?

my script is the following:

vcontact2 --raw-proteins proteins.faa --rel-mode <E2><80><98>Diamond<E2><80><99> --proteins-fp gene2genome.csv  --db 'ProkaryoticViralRefSeq94-Merged' --pcs-mode MCL --vcs-mode ClusterONE --c1-./cluster_one-1.0.jar --output-dir ./vcontact2_out/

Any guidance on fixing it?

Thanks in advance!!

[Ping Gao]

I used pip to uninstall numpy and pip install numpy with version 1.23.1 or other older version. You may try

[Qunk Fang]

Have you solved the problem? I encountered the same problem. Change numpy version can’t help me.

[Cartr Merenstein]

I also had this issue and solved it with an earlier numpy version. Did you try a clean install?

I deleted my conda environment then made a new one, python version 3.7. I installed numpy 1.20.1 with conda, then installed vcontact2 and MCL. It took a while to solve the install but it seems to be working now.

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Hope that helps

[Ivan Pchelin]

@Cartr Merenstein Thank you, it really helped very much. For somebody else, I installed the thing on Ubuntu 23.10 with the following:

mamba create -n vcontact-env python==3.7
mamba activate vcontact-env
mamba install numpy==1.20.1
mamba install -y -c bioconda vcontact2 mcl blast diamond

The file cluster_one-1.0.jar can be downloaded from https://paccanarolab.org/cluster-one/

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