Error in core metrics ( tree must have a branch lenghth)

[Nicholas_Bokulich]

Thanks for reporting, @rparadiso!

First, have you tried the fix reported here?

Greengenes Tree Download With Branch Lengths

Hi @Stephanieorch, The issue comes from the reroot performed on that release of Greengenes where the added branch did not get set with a length (connecting "k__Bacteria" to a common vertex with "k__Archaea"). In QIIME1, this missing length was not an issue as PyCogent's PhyloNode interpreted a missing length as 0.0 when computing phylogenetic metrics so this went unnoticed at the time of release. One way to solve this is to open the tree, set a length, and write it out. An example of doing so i…

Alternatively, this is a fix that you can do by just opening the file in a text document, as opposed to trying to work with python:

Error with imported sepp tree in qiime2 diversity analyses

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’…

Please describe what you've tried or give those a try, and we can go from there!

Thanks!