unexpected keyword argument 'choice'

[orctyr]

Hi,

I had installed arg_ranker succesfully including requirements.
But there is something error when I try test data.

Details:

$ arg_ranker -i $path/arg_ranker/test -kkdbtype standard -kkdb $path/arg_ranker/db/k2_standard_20210517/

arg_ranker evaluates the risk of ARGs in genomes/metagenomes
Requirement: blast, diamond, kraken, python 3
Optimal: a table of the metadata of your samples (see example/All_sample_metadata.txt).
Copyright:An-Ni Zhang, MIT; Prof. Tong Zhang, University of Hong Kong
Contact caozhichongchong@gmail.com

Traceback (most recent call last):
File "$path/arg_ranker/bin/arg_ranker", line 8, in
sys.exit(main())
File "$path/arg_ranker/lib/python3.8/site-packages/arg_ranker/main.py", line 64, in main
optional.add_argument('-kkdbtype',
File "$path/arg_ranker/lib/python3.8/argparse.py", line 1368, in add_argument
action = action_class(**kwargs)
TypeError: init() got an unexpected keyword argument 'choice'

Could you please give some suggestions?
Many thanks.
orctyr

[JorgeQL]

Hello,

I obtained the same error message when I tried to run the command line. Could you please help us?

Many thanks,

Jorge

[caozhichongchong]

Hi orctyr and Jorge,

Thank you so much for reaching out!
Sorry about this late reply.

I have adjusted and updated the code.
Please re-install the newest arg_ranker (v2.8.3) by running
pip uninstall arg_ranker
pip install arg_ranker

Thank you again!

Best regards,
Anni

[caozhichongchong]

Hi orctyr and Jorge,

I have noticed an error of arg_ranker.v2 when reporting the total ARG abundance in metagenomes.
If the total ARG abundance is used in your research, please refer to https://github.com/caozhichongchong/arg_ranker for more details!
I'm really sorry about this inconvenience!
Please feel free to reach out to me if you have any questions.

Best regards,
Anni

[orctyr]

Thank you very much.

[JorgeQL]

Dear Anni, Thank you for your reply! Best regards, Jorge Jor El jue, 30 jun 2022 a las 14:19, Anni Zhang ***@***.***>) escribió:

…

Hi orctyr and Jorge, I have noticed an error of arg_ranker.v2 when reporting the total ARG abundance in metagenomes. If the total ARG abundance is used in your research, please refer to https://github.com/caozhichongchong/arg_ranker for more details! I'm really sorry about this inconvenience! Please feel free to reach out to me if you have any questions. Best regards, Anni — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVKGRQ3HPKHZ6B42LDZCKSDVRXQKJANCNFSM5CLSCXSQ> . You are receiving this because you commented.Message ID: ***@***.***>