You are right. Either add that strain to your fasta and metadata, or supply it as an additional input in builds.yaml
inputs:
- name: "root_ref" # or however you want to call it
metadata: "data/references_metadata.tsv"
sequences: "data/references_sequences.fasta"
The sequence and metadata are in the ncov/data folder that comes with the repo.
Just to be comprehensive, the root strain needs to be in the include.txt (for example, the default one that is in ncov/defaults/include.txt) so it doesn’t get subsampled out in any case. Unless you supply your own include.txt, this is usually not a concern.