Invalid value for '--i-reference-database

[Pmoa (Ravi)]

Hello,

I am relatively new to QIIME 2.
I am trying to build a phylogenetic tree using an external reference database for functional target gene pmoA(methanotrophs).

This is my command:

qiime fragment-insertion sepp
--i-representative-sequences rep_seq_pm5.qza
--i-reference-database pmoa7809.qza
--o-tree pm_tree.qza
--o-placements pm-placements.qza
--p-threads 16

This is the error I am getting:

(1/1) Invalid value for '--i-reference-database':
Expected an artifact of at least type SeppReferenceDatabase.
An artifact of type FeatureData[Sequence] was provided.

I am aware of the fact that my reference databases is of type FeatureData[Sequence], but I am not sure how to change it to type SeppReferenceDatabase. OR how can I build phylogenetic tree using the FeatureData[Sequence] or any other method?

Thank you so much for the help!

[cherman2 (Chloe Herman)]

Hello @Pmoa,
Welcome to the forum!

I am not sure how to build a SeppReferenceDatabase from FeatureData[Sequence], I have looked into it before and I think you can't. Here is another thread on the forum taking about this issue

But you can just build a phylogeny using you rep-seqs using align-to-tree-mafft-fastree. Here is an example from the “Moving Pictures” tutorial — QIIME 2 2022.2.0 documentation.

Hope this helps!

[Pmoa (Ravi)]

Hello @cherman2,

I will try to build the tree using 'align-to-tree-mafft-fastree'
Thank you for the recommendation!