search

KennthShang / PhaBOX

Local version of the virus identification and analysis web server (tool set)
https://phage.ee.cityu.edu.hk/
Academic Free License v3.0
37 stars 5 forks source link

Error in Bio.Application and how to build better command line with the subprocess module #24

Closed XuyingZhu closed 1 month ago

XuyingZhu commented 2 months ago

Dear PhaBox team, Thanks for such an amazing tool. However, I had a problem when testing four functions of PhaBox. I was suggested to build a command line with the subprocess module. Would you please give some advice on the new command or other ways to solve this problem? Thank you, and I am looking forward to your recent reply! My commands are: export PATH=$PATH:/share/home/zhuyy/software/PhaBOX-main

run PhaMer

python /share/home/zhuyy/software/PhaBOX-main/PhaMer_single.py --contigs /share/home/zhuyy/software/PhaBOX-main/test_contigs.fa --threads 48 --len 3000 --rootpth simple_test --out PhaMer_out/ --dbdir database/ --parampth parameters/ --scriptpth scripts/

run PhaTYP

python /share/home/zhuyy/software/PhaBOX-main/PhaTYP_single.py --contigs /share/home/zhuyy/software/PhaBOX-main/test_contigs.fa --threads 48 --len 3000 --rootpth simple_test --out PhaTYP_out/ --dbdir database/ --parampth parameters/ --scriptpth scripts/

run PhaGCN

python /share/home/zhuyy/software/PhaBOX-main/PhaGCN_single.py --contigs /share/home/zhuyy/software/PhaBOX-main/test_contigs.fa --threads 48 --len 3000 --rootpth simple_test --out PhaGCN_out/ --dbdir database/ --parampth parameters/ --scriptpth scripts/

run CHERRY

python /share/home/zhuyy/software/PhaBOX-main/Cherry_single.py --contigs /share/home/zhuyy/software/PhaBOX-main/test_contigs.fa --threads 48 --len 3000 --rootpth simple_test --out Cherry_out/ --dbdir database/ --parampth parameters/ --scriptpth scripts/

And the error message is as follows: /share/home/zhuyy/anaconda3/lib/python3.11/site-packages/Bio/Application/init.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules.

We instead now recommend building your command line and invoking it directly with the subprocess module.

Best wishes, Xuying Zhu

KennthShang commented 2 months ago

Hi there,

This is just a warning message and you do not need to do anything. The program can be run correctly.

If you want to remove warning message, you can downgrade your python environment or reinstall it using 

conda create -n PhaBOX phabox=1.1 -c bioconda -c conda-forge -c pytorch -c jyshang2

Best, Jiayu

XuyingZhu commented 2 months ago

Hi Jiayu, Thank you for your reply. I have reinstalled it and run the program successfully. Best wishes, Xuying Zhu

KennthShang commented 1 month ago

Hi Xuying,

Our PhaBOX has been upgraded into 2.0 version with more powerful usage. Please check the guidelines!

Best, Jiayu

XuyingZhu commented 1 month ago

Hi Jiayu,

Thank you for telling me the updated information. I will keep using this helpful tool!

Best wishes, Xuying Zhu