treetime.UnknownMethodError: TreeTime.reroot – ERROR: unsupported rooting mechanisms or root not found
We’ve most commonly run into this when trying to root the tree using a sample which has been filtered out in previous steps, or which may not have been included in the starting dataset. The default config uses “Wuhan/Hu-1/2019” but other pipelines use “Wuhan-Hu-1/2019”. Both are in the default include.txt so that they doesn’t get filtered. Without seeing your pipeline I don’t know if you are using a different root, a different include.txt, or are using a sample which doesn’t exist in your dataset to begin with.
is it required to keep the “date_submitted” column always in metadata?
It shouldn’t be, but currently a few of our scripts require this (e.g. scripts/diagnostic.py which caused the error in the original post). We’ll try to improve this.