Commands Not Working

Hi everyone,

I have tried searching through the forums and even found some threads that I thought might answer my question, so I followed them completely / to a tee with no luck.

I'm having problems running any commands on QIIME2. I'm currently running qiime2-2021.4, and no matter the command I run, I get an error message saying "-bash command not found". It's happening with literally every command.

Other questions on the forum say that this is probably a problem with qiime2 needing to be updated, but I can't even follow the codes that they suggest because it simply says command not found. Here is the thread I followed: Qiime2 not Working

I should say that last week I ran qiime2 very fluidly without any problems, but my computer must have updated since.

I'd appreciate any help I could get. I'm quite new to bioinformatics. Thanks!

Hello Sam,

Welcome to the forums! :qiime2:

What other clues can you give us about your setup? Are you using Mac or Windows and what version are you running? How did you install Qiime2?

Hi Colin!

I am using MacOS Monterey version 12.0.1. I installed Qiime2 using conda.

Also, I forgot to mention this in the original post, but when I activate qiime2 through conda, it immediately gives me an error saying

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Not sure if this helps at all

Try installing xcode, as shown here:

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Hi Colin, thanks for your help. This worked!


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