Augur refine error: unsupported rooting mechanisms

Hello, this is happening with the example builds as well as my own. I’ve reinstalled the nextstrain environment once already,

augur refine is using TreeTime version 0.8.2

0.66 TreeTime.reroot: with method or node: Wuhan/Hu-1/2019
Traceback (most recent call last):
File “/home/gabrielp/miniconda3/envs/nextstrain/bin/augur”, line 10, in
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/”, line 10, in main
return argv[1:] )
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/”, line 75, in run
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/”, line 206, in run
tt = refine(tree=T, aln=aln, ref=ref, dates=dates, confidence=args.date_confidence,
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/”, line 42, in refine
tt.clock_filter(reroot=reroot, n_iqd=clock_filter_iqd, plot=False) #use whatever was specified
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/treetime/”, line 345, in clock_filter
self.reroot(root=‘least-squares’ if reroot==‘best’ else reroot, covariation=False, clock_rate=fixed_clock_rate)
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/treetime/”, line 471, in reroot
raise UnknownMethodError(‘TreeTime.reroot – ERROR: unsupported rooting mechanisms or root not found’)
treetime.UnknownMethodError: TreeTime.reroot – ERROR: unsupported rooting mechanisms or root not found

Could it be this one? Automatically include reference metadata and sequence for TreeTime root · Issue #700 · nextstrain/ncov · GitHub

Did you include Wuhan/Hu-1/2019 metadata and sequences in your input data?

This looks like my issue thank you!

How should I include the Wuhan/Hu-1/2019 metadata and sequences? Another set of inputs in the build file or add the sequence to my fasta and tsv?

You are right. Either add that strain to your fasta and metadata, or supply it as an additional input in builds.yaml

  - 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.

1 Like

one potential reason might be that there are different variations of the name out there (Gisaid vs genbank). Some call it Wuhan/Hu-1/2019, other Wuhan-Hu-1/2019.