I have run the q2-sample-classifier and am receiving an error that for such option for the output visualization. Any thoughts on why this might be occurring? qiime sample-classifier classify-samples --i-table C:\Users\kjharris\Desktop\crayfishmicrobiome2018\rep-seqs.qza --m-metadata-file "C:\Use…

Hey there @mudbugecology ! [image] mudbugecology: Any thoughts on why this might be occurring? Yes indeed - the information is all right there, ripe for the picking! :pear: :apple: Let's start with the error message: [image] mudbugecology: Error: no such option: --o-visualization Oka…

Thanks for the quick reply! I will give this a try!

Hey @mudbugecology , Just to clarify: "visualization" was an output in an old version of q2-sample-classifier. You must have been using some old docs or copying/pasting from an old collection of scripts. So you are not going crazy — but as @thermokarst recommends whenever you see an error like that …

I am attempting to run this in Linux as a subsystem on a new pc and I have the most recent release of q2, I have also been attempting this on my mac, but I am still having some difficultly getting the directory to output: (qiime2-2019.4) kjharris@6SS4NV2:/mnt/c/Users/kjharris/Desktop$ qiime diversi…

[image] mudbugecology: qiime sample-classifier classify-samples not sure why I started it that way since the current doc on the tutorial Predicting sample metadata values with q2-sample-classifier — QIIME 2 2019.4.0 documentation suggests this: qiime sample-classifier classify-samples --i-…

Hi @mudbugecology , [image] mudbugecology: Linux as a subsystem on a new pc I think the issue is you need to prefix your paths with /mnt/c/<normal path here, but with / not \>. That being said, the parser shouldn't really be complaining about those options not existing, as obviously they do.…

thanks, Evan!! I will give this a go and let you know if it works

working on a new error message, but this seems to be moving in the right direction: qiime sample-classifier classify-samples --i-table /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/table/qza --m-metadata-file /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata may 1 2019 modified…

Yep! The issue this time is one of path quoting, to be honest, I'm taking notes here, as this is another common problem that ideally the parser should be handling more gracefully (so thanks!) To solve this one you have two options: /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata may…

bingo! you all are the best qiime sample-classifier classify-samples --i-table /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/table-rarefy-to-12000.qza --m-metadata-file /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata\ April\ 30\ 2019.t xt --m-metadata-column SampleType --…

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Error: no such option: --o-visualization q2-sample-classifier

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