execution problem about platon

[oschwengers]

Hi @kimTina321 ,
I tested Platon v1.7.0 in a fresh conda environment and database via:

mamba create -p ./conda platon=1.7.0
wget https://zenodo.org/record/4066768/files/db.tar.gz
tar -xzf db.tar.gz
platon --db ./db --prefix test --output test --verbose test-genome.fna

It ran smoothly without any error or issue.

[kimTina321]

Hi @kimTina321 , I tested Platon v1.7.0 in a fresh conda environment and database via:

mamba create -p ./conda platon=1.7.0
wget https://zenodo.org/record/4066768/files/db.tar.gz
tar -xzf db.tar.gz
platon --db ./db --prefix test --output test --verbose test-genome.fna

It ran smoothly without any error or issue.

Hi, @oschwengers . I ran what you did, but I still met the error message below. Sorry for bothering you again. Besides, I tried to download plasmidFinder before and met the similar error of numpy.

Traceback (most recent call last):
File "/home/liu/conda/bin/platon", line 6, in
from platon.platon import main
File "/home/liu/conda/lib/python3.11/site-packages/platon/platon.py", line 12, in
from Bio import SeqIO
File "/home/liu/.local/lib/python3.9/site-packages/Bio/SeqIO/init.py", line 374, in
from Bio.Align import MultipleSeqAlignment
File "/home/liu/.local/lib/python3.9/site-packages/Bio/Align/init.py", line 29, in
raise MissingPythonDependencyError(
Bio.MissingPythonDependencyError: Please install numpy if you want to use Bio.Align. See http://www.numpy.org/

[oschwengers]

I'm sorry, I cannot reproduce this error. It seems like you have a mixture of different Python versions within your Conda environment: Python 3.11 and 3.9 what should not be the case.

As this is not related to Platon but the Conda setup, may I kindly refer you the the official Conda / Bioconda docs?
Therefore, I'll close this now but please, do not hesitate to re-open it or a new issue in any case.
Thanks and kind regards!