q2-fragment-insertion - assigning taxonomy

[Nicholas_Bokulich]

Welcome to the forum @Jennifer_Bell!

First, I am assuming you have seen this post and the other warnings about this experimental method:

q2-fragment insertion problems with Silva 128 taxonomy

Welcome to the forum @Rkubinski! Could you please provide the commands that you are running and the full error message (though that message seems clear enough, the full message may provide better context). I should add a word of warning: that method is experimental and does not really perform particularly well for taxonomy classification, so I would really recommend using the methods in q2-feature-classifier instead.

Second, it looks like that file was deleted so the tutorial is out of date (I have raised an issue to get this fixed). For now you might be able to access the old file here but I can't guarantee if that will work (sorry! I am not a fragment-insertion developer but maybe @Stefan can help if that file does not work)

@Jennifer_Bell

May I use the reference taxonomy I trained for my primers?

No — that trained classifier is specific to the qiime feature-classifier classify-sklearn method. It cannot be used with fragment-insertion.

@Jennifer_Bell

Is this reference taxonomy 16S (515F/806R) specific? I’m guessing so since the previous parts of the workflow referenced the moving pictures tutorial, but it is not clear.

Yes, it uses Greengenes, which is 16S-specific

@Jennifer_Bell

Finally, it appears that the file phylogeny.qza is not a standard .nwk tree file which I will need for further analysis (specifically calculating MNTD using the picante package). Is there was way to create this?

What happens if you use qiime tools export? The exported file should be .nwk

Good luck!