Since this is not strictly relevant to this topic (it is an issue with that specific reference tree and, e.g., you could use a different reference tree), do you want to open up a separate topic to solve your q2-fragment-insertion issue? If that solution is relevant to the current discussion, we can link back to that here.
@Lauren and I have been trying to troubleshoot this too, but with no luck so far. We got the same error as you when we repeated what you did, and also when we tried the same code but after importing the XX_otus_unannotated.tree.
We aren't sure how to use Python to fix the branch length issue as shown in the post that @Nicholas_Bokulich linked to - our computing cluster does have Python built in but we haven't been able to figure out how to actually use it yet .
We look forward to your thread on this and will plan to chime in there!
Hi everyone, @rparadiso was able to solve the greengenes branch length issue in a separate topic — see here for a few different solutions:
@cjone228 that topic lists some other options — opening and manually modifying the file, or running a python script in the bash shell (command line), so there are a few options to suit whatever you feel most comfortable working with.
Please post to that topic if you have any follow-up questions or run into any issues with fixing your tree(s).