compdef output when activating qiime2

I just installed qiime2 and when I source activate it (source activate qiime2-2020.2), it gives me the following output:

complete:13: command not found: compdef

But I don’t think this is an error; after it gives that command, it runs qiime normally and seems like everything is working. Should I just disregard that compdef output? I’m not sure if that output is affecting how qiime2 is working.

Hello @moonsun,

Welcome to the forums! :qiime2:

Do you know shell you are using? Most of my linux systems use bash, and my MacBook uses zsh by default. A quick google makes me think this might be an issue with the ohmyzsh shell.


Hi Colin,

Thanks for your reply. My MacBook is running zsh but I managed to find a way to change default shell from zsh to bash. However, when I now run it on bash and source activate qiime2, it gives the following output error:

-bash: activate: No such file or directory

Not sure if I should keep running it on zsh and ignore the compdef output. Thanks

You may have to initialize conda with conda init to get these commands to work.

This should work on both zsh and bash… so let’s see if conda init fixes the problem!


I just installed qiime2 on a new macbook pro and came across this problem. This fixed it for me: