I have been using QIIME 1 for a while now and I’m finally switching to QIIME2 out (v 2019.1). I was trying to compare Q1 and Q2 OTUs with ASVs but I’m having some problems when running Sepp for the phylogenies constructed from OTUs. I used QIIME2 from scratch to create the rep_set qza with the open-reference pipeline. The thing is, sepp carries out some checking step in which it decides I have repeated tips and aborts the phylogeny construction.
I’ve looked down in the forums and it seemed to me it could be something weird about some of my rep seqs having the same name (number, actually) as the reference I used (green genes 2013_08), so I altered the names of each of them (added a set of characters as prefix) and sepp runned without errors (sorry but I did not save the original error it prints).
Now, when working with the core-metrics pipeline, I tried importing a tree from Q1 and had a similar problem as it prints the following error traceback:
File “/home/rodrigo/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/diversity/_util.py”, line 93, in _validate_otu_ids_and_tree
raise DuplicateNodeError(“All tip names must be unique.”)
skbio.tree._exception.DuplicateNodeError: All tip names must be unique.
I checked my files and they are in fact unique nemes, both in the table and the trees. I then changed the names in my otu tables to match those in my sepp newick tree and it worked again.
There seems to be some odd behaviuour in the _validate_otu_ids_and_tree algorithm that does not allow it to continue. I’ve already figured out how to get around this but could you look at it so it can get fixed in later versions, please?