Hello, 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 phyloge…

Hi @aeriel.belk ! [image] aeriel.belk: All non-root nodes in tree must have a branch length. 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 …

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 importe…

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-di…

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 …

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!

QIIME 2 Forum

Error with imported sepp tree in qiime2 diversity analyses

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sepp, phylogeny, tree, core-metrics, fragment-insertion

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