Hello, I would like to generate PCoA plots. Some of my samples do not have a value for the category that I am using for the thirs PCoA axis, whichis "Exper.Day" and I was receiving an error message telling me this. Therefore, I deleted those samples from my metadata file and renamed my metadata fil…

Hi. I installed Qiime2 via Virtual Box in August following the instructions posted on Installing QIIME 2 using VirtualBox — QIIME 2 2017.8.0 documentation .... So I don't know how I would have ended up with an older version of Qiime2? Did it just recently get updated? It says "qiime2@qiime2core2017-…

By the way, the variables "Treatment", "Exper.Day, and "Morning pH" are all numerical whereas"Replicate" is categorical and can be A,B,C,D,E, or F. I originally had "Treatment" be categorical as "High pH" or "Low pH" but then changed it to numerical because some of the alpha diversity analyses requ…

Hi @Lisa_Crummett ! [image] Lisa_Crummett: So I don’t know how I would have ended up with an older version of Qiime2? Maybe you copied the wrong link in the download section? QIIME 2017.6 was the current release version at the QIIME 2 Las Vegas workshop, so maybe you had grabbed the old relea…

Hi Matt. I did install the latest version of Qiime2 in late August when following the instructions on the website for installing Qiime2 using virtual box. I went back and checked the instructions and the screen shots show Qiime2 Core - 2.0.6. Is it possible that Qiime 2 2017.8 was not made available…

[image] Lisa_Crummett: I went back and checked the instructions and the screen shots show Qiime2 Core - 2.0.6 A few screenshots do show that, but there is also a note in the docs, copied here: Note, the list of installed plugins (and their versions) will likely differ depending on the versi…

HI Matt, Yes, the metadata file did get tweaked when I cut and pasted it into my reply to you. It does in fact have tabs in it. I just got the latest version of Qiime2 natively installed on a MacBook Pro so I will have a go at this command using this new set up and see how it goes...

I successfully validated my metadata file using the Keemei and it said that it was a valid Qiime2 mapping file. And yet when I run the command below using the latest version of Qiime2 (2017.8) I get a ValueError saying that, "%s is not a QIIME archive." % filepath..... metadataonlymesocosm2.txt is n…

[image] Lisa_Crummett: Non-string Metadata index values detected Hi @Lisa_Crummett - this is interesting --- can you please provide your metadata file so that we can figure out why things look okay to Keemei but not to QIIME 2? If you can do this, feel free to send to me in a direct message. …

Sure, I have attached my metadata file. Cheers, Lisa metadataonlymesocosm2.txt (1.2 KB)

Hi @Lisa_Crummett ! Thanks for sharing your metadata, that was really helpful! The problem is that your metadata file has several empty rows near the bottom. I took a screenshot of your file opened in my text editor, with some additional syntax highlighting turned on: [18 PM] The error message yo…

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Error in command for generating PCoA plot

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