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caozhichongchong / arg_ranker

MIT License
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unexpected keyword argument 'choice' #1

Closed orctyr closed 3 years ago

orctyr commented 3 years ago

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 commented 3 years ago

Hello,

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

Many thanks,

Jorge

caozhichongchong commented 3 years ago

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 argranker

Thank you again!

Best regards, Anni

caozhichongchong commented 2 years ago

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 commented 2 years ago

Thank you very much.

JorgeQL commented 2 years ago

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

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