I am running q2cli version: 2019.10.0 installed via conda
I am trying to build an ITS phylogenetic tree with
$ qiime fragment-insertion sepp --i-representative-sequences ./training-feature-classifiers_ITS/rep-seqs-dada2-ITS-without-recaps.qza --i-reference-database sh_refs_qiime_ver8_99_s_04.02.2020.qza --o-tree tree_ITS_without_recaps.qza --o-placements tree_placements_ITS_without_recaps.qza --p-threads 24
but I get the error message:
(1/1) Invalid value for “–i-reference-database”: Expected an artifact of at least type SeppReferenceDatabase. An artifact of type FeatureData[Sequence] was provided.
which is fair enough since I used qiime tools import --type FeatureData[Sequence]… to import the .fasta file. I’m sure the answer is right in obvious, but I can’t find it for two days for this question: how, then, do I turn the UNITE files into a SeppReferenceDatabase .qza?
Then I see on the ITS tutorial Fungal ITS analysis tutorial the admonition to use ITS only for species ID, not for phylogentic diversity methods. It suggests the q2-ghost-tree plugin as an alternative, but that tutorial also cautions against its use for trees, so which is it?