Augur refine error: unsupported rooting mechanisms

Help and Getting Started
1

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
sys.exit(main())
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/main.py”, line 10, in main
return augur.run( argv[1:] )
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/init.py”, line 75, in run
return args.command.run(args)
File “/home/gabrielp/miniconda3/envs/nextstrain/lib/python3.8/site-packages/augur/refine.py”, 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/refine.py”, 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/treetime.py”, 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/treetime.py”, 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

2

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?

3

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?

4

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.

1 Like
5

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.