First-time qiime2 user with 1.9.1 qiime biom table ran into mafft error unsure if workflow is correct

[jwdebelius (Justine Debelius)]

Hi @mercadocapote,

Check out this post, it looks like a similar error and possible solution.

Best,
Justine

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…