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?.
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!
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.
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!
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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