Hi there, I'm trying to run my alpha/beta diversity analysis using core-metrics-phylogenetic command. Here is my script: qiime diversity core-metrics-phylogenetic --i-phylogeny diversity_analysis/rooted-tree.qza --i-table deblur/table.qza --p-sampling-depth 7095 --m-metadata-file deblur/me…

Welcome @xchromosome ! It does look like you are doing everything correct! But I am sure there is an easy (if cryptic) solution. A couple ideas come to mind: Perhaps you are using an old version of QIIME 2? Please confirm what version you are running. If you are copying/pasting commands from the i…

Hi Nicholas, Thanks for your help. I am running version 2019.1 on Virtual Box (version 6.0.4). I had typed it out in the terminal directly, but I shut down my virtual machine and tried again from scratch as suggested. No luck! :cry: I have actually encountered this problem a few times during my a…

Hi! Just try --output-dir instead of --o-output-dir :wink:

good call @timanix ! I did not catch that.

D'oh! So simple! :woman_facepalming: Thank you both!

QIIME 2 Forum

Error: no such option: --o-output-dir

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