Closed orctyr closed 2 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
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
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
Thank you very much.
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 https://github.com/caozhichongchong/arg_ranker/issues/1#issuecomment-1171534832, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVKGRQ3HPKHZ6B42LDZCKSDVRXQKJANCNFSM5CLSCXSQ . You are receiving this because you commented.Message ID: @.***>
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