Cannot add taxonomy to a rooted tree (created using the fragment insertion plugin) in ITOL


(Fernando Studart) #1

Hi Everyone,

I’m getting familiar with the q2-fragment-insertion plugin, now available in qiime 2019.1
I was able to follow the tutorial and generate the tree (note: this plugin does not seem to work in WSL, I had to use Virtualbox in my windows system, in which it ran with no problems).
After that, I exported the SEPP tree to obtain the file in *.nwk format. Then, I uploaded the tree to ITOL with no problems. When I try to add the taxonomy file, as the tips in the uploaded tree no longer contain the ASV hast tags (it has some numbers, though), I receive this message: “Couldn’t find ID 01e51045bda814ec780fcfb7613ccc1b in the tree”. With the original tree (before using the fragment insertion plugin), I didn’t have any issues.

Interestingly, I can merge the new tree with the BIOM file (created from my data) in the phyloseq package with no problems.

I really appreciate any advice on this.

Thanks,
FS


(Nicholas Bokulich) #2

Hi @fstudart,
I am not sure whether this is an issue with q2-fragment-insertion or iTOL. Sounds like maybe iTOL is the problem, if it is changing the tip labels, since you can merge in phyloseq without issue.

@iletunic do you have any thoughts on what is going on here? (and if this is an iTOL error and you prefer to provide support through another channel please feel free to redirect this conversation there).

Thanks!


(Ivica Letunic) #3

Does not sound like an ITOL error. If you are uploading Newick trees directly, you’re no longer using iTOL’s Qiime support. What do you mean by ‘taxonomy file’ which is giving you the error? ITOL LABELS annotation file?

Send me the files directly and I’ll take a look.