Installing QIIME 2-2020.2 on Mac Catalina, error " complete:13: command not found: compdef”

I haven’t found the answer to this in the QIIME2 forum yet, sorry if I have missed it!
Here are my specs:
-Running Miniconda 3 on macOS Catalina v10.15.4
-Installed qiime2-2020.2

Question 1. When activating conda, although the below error message pops up, qiime is activated and I managed to run commands such as “qiime info”. Is this ok?

(base) [email protected] ~ % conda activate qiime2-2020.2

complete:13: command not found: compdef
(qiime2-2020.2) [email protected]_64-apple-darwin13 ~ % qiime info
System versions
Python version: 3.6.7
QIIME 2 release: 2020.2
QIIME 2 version: 2020.2.0
q2cli version: 2020.2.0

Installed plugins
alignment: 2020.2.0
composition: 2020.2.0
cutadapt: 2020.2.0
dada2: 2020.2.0
deblur: 2020.2.0
demux: 2020.2.0
diversity: 2020.2.0
emperor: 2020.2.0
feature-classifier: 2020.2.0
feature-table: 2020.2.0
fragment-insertion: 2020.2.0
gneiss: 2020.2.0
longitudinal: 2020.2.0
metadata: 2020.2.0
phylogeny: 2020.2.0
quality-control: 2020.2.0
quality-filter: 2020.2.0
sample-classifier: 2020.2.0
taxa: 2020.2.0
types: 2020.2.0
vsearch: 2020.2.0

Application config directory

Getting help
To get help with QIIME 2, visit
(qiime2-2020.2) [email protected]_64-apple-darwin13 ~ %

Question 2. When try to enable tab completion, running the code with conda tab-qiime below gave an error, and using source tab-qiime, the error in question 1 came back.

*(qiime2-2020.2) [email protected]_64-apple-darwin13 ~ % autoload bashcompinit && bashcompinit && conda tab-qiime *

CommandNotFoundError: No command ‘conda tab-qiime’.

(qiime2-2020.2) [email protected]_64-apple-darwin13 ~ % autoload bashcompinit && bashcompinit && source tab-qiime

complete:13: command not found: compdef
(qiime2-2020.2) [email protected]_64-apple-darwin13 ~ %

Thank you for your help, I am a bit of a coding and command language noob (!)

Hi @charlene

Both of these issues look pretty suspicious to me, I’m not sure your CLI environment is set up in a “traditional” manner. Let’s take a closer look, please run both of the following commands, and copy-and-paste the results here:


echo $0

Once I have more info I can comment specifically on the questions you asked. Thanks!


A post was split to a new topic: Trouble installing QIIME 2 2020.8