Errors after running alpha diversity oberserved otus

Hello, I have an error coming out when I want to analyze alpha diversity by using "qiime diversity alpha --i-table deblur_rare_ff_table.qza --o-alpha-diversity alpha_diversity/alpha_diversity_obs --p-metric observed_otus".

Below is the error:
Plugin error from diversity:

Parameter 'metric' received 'observed_otus' as an argument, which is incompatible with parameter type: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_features', 'osd', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles', 'strong')

Debug info has been saved to /var/folders/bd/23cxg4y948s9566jg0d66prh0000gp/T/qiime2-q2cli-err-hcu4h2zd.log

By the way, I am using q2cli version 2022.8.0 in the environment of anaconda3.

I would appreciate it if someone could give me some hints to solve this error. Thanks a lot.

Hello and welcome to the forum!
In newer versions of Qiime2 "observed_otus" metric was renamed to the more appropriate "observed_features" to avoid confusion that may arise by the naming inconsistency. Just modify accordingly the script to fix the error.


1 Like

Hello timanix,

Thank you so much for your help. Feedback: It works very well.