Error when using sepp with vsearch clustered rep-seqs

[Nicholas_Bokulich]

@Ryuk

I am a rookie so actually don’t know how to use the greengene reference after closed-reference OTU to generate tree.qza . So I would be really grateful if you could give me a clue.

The greengenes releases come with a bunch of reference trees. Choose the correct tree (matches the reference sequences that you used for closed-reference OTU clustering) and import to QIIME 2 as described here (but as a Rooted tree):
https://docs.qiime2.org/2019.10/tutorials/importing/#phylogenetic-trees

@Ryuk

I run the command with --p-debug option and here’s the results：

Thanks for sharing that info! Looks like the problem is actually pretty straightforward:

@Ryuk

ValueError: Your input fragment file contains 212 sequences, whose names overlap with names in your reference. Please rename your input fragments and re-start.

So doing closed-reference OTU clustering and then attempting to graft those fragments into a tree does not work because those sequences are already in the tree and tip names must be unique... so this is not a bug, this is just a sensible error to prevent improper use of SEPP.

Import that tree instead of using SEPP. Good luck!