Error with imported sepp tree in qiime2 diversity analyses


I am trying to use an imported tree created in sepp to run the qiime diversity core-metrics-phylogenetic analysis. I received the error:

Plugin error from diversity: All non-root nodes in tree must have a branch length.

I followed the importing protocol for a tree e.g.
Importing a phylogenetic tree created using the SEPP package, rooted or unrooted?.

Hi @aeriel.belk!

That error sounds like the tree you imported from sepp is missing the branch lengths on some (or all) of the nodes. I am not familiar with sepp, so I would check with their support team for advice on how to export a tree with all of the branch lengths included. Would you able able to share your tree with me? You can send in a DM if you are unable to post it publicly. Thanks! :t_rex:

Hi, thanks for getting back to me so quickly!

I will definitely check with the sepp team to try to resolve this.
Thanks for looking at my tree in the meantime! The link to a dropbox folder is below (because I can’t upload it in this file format). It contains both the sepp tree and the tree imported into qiime2.


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Thanks so much for the files!

Have you had a chance to check out the community plugin, q2-fragment-insertion? This community plugin wraps sepp, which should help out with what you are working on.

I was perusing the source code for this community plugin and noticed the following comments:

Beta-diversity computation with Qiime2 requires every branch to have a length, which is not necessarily true for SEPP produced insertion trees. Thus we add zero branch length information for branches without an explicit length.

I think that means my earlier hunch was correct about not all branches having a length, but fortunately, the q2-fragment-insertion plugin looks like it can do the cleanup for you to make sure this phylogenetic tree is compatible with downstream QIIME 2 analyses. Keep us posted! :t_rex:


Hi Aeriel,
I worked on the q2-fragment-insertion plugin, which wraps SEPP and I want to encourage you to use it since it handles those types of complications plus its using the latest version of the code which reduces the memory footprint a lot.

To save you some computation, you can manually edit your newick tree file. All you need to do is jump to the very end of the one line and add a branch length to the k__bacteria, i.e. “:0.0965499)‘k__Bacteria’);” need to become “:0.0965499)‘k__Bacteria’:0.0);”


Thank you both for your input!

I was able to successfully use my tree when I followed @Stefan’s suggestion to manually edit my tree file, I’m glad there was such a simple way to solve my problem.

Thank you again for your assistance!

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