# Augur refine error: unsupported rooting mechanisms

**URL:** <https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653>\
**Category:** Help and Getting Started\
**Created:** [August 10, 2021, 5:39pm UTC](https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653 "2021-08-10T17:39:25Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![gabriel](https://avatars.discourse-cdn.com/v4/letter/g/9de0a6/32.png) [@gabriel](https://nextstrain.discourse.group/u/gabriel)\
**Post date:** [August 10, 2021, 5:39pm UTC](https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653/1 "2021-08-10T17:39:25Z")

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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

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<div class="post-metadata">

**Author:** ![dlu](https://avatars.discourse-cdn.com/v4/letter/d/e36b37/32.png) [@dlu](https://nextstrain.discourse.group/u/dlu)\
**Post date:** [August 10, 2021, 5:43pm UTC](https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653/2 "2021-08-10T17:43:23Z")

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Could it be this one? [Automatically include reference metadata and sequence for TreeTime root · Issue #700 · nextstrain/ncov · GitHub](https://github.com/nextstrain/ncov/issues/700)

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

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<div class="post-metadata">

**Author:** ![gabriel](https://avatars.discourse-cdn.com/v4/letter/g/9de0a6/32.png) [@gabriel](https://nextstrain.discourse.group/u/gabriel)\
**Post date:** [August 10, 2021, 8:39pm UTC](https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653/3 "2021-08-10T20:39:00Z")

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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?

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<div class="post-metadata">

**Author:** ![dlu](https://avatars.discourse-cdn.com/v4/letter/d/e36b37/32.png) [@dlu](https://nextstrain.discourse.group/u/dlu)\
**Post date:** [August 11, 2021, 3:19pm UTC](https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653/4 "2021-08-11T15:19:48Z")

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

```auto
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.

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<div class="post-metadata">

**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [August 12, 2021, 11:17am UTC](https://nextstrain.discourse.group/t/augur-refine-error-unsupported-rooting-mechanisms/653/5 "2021-08-12T11:17:57Z")

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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`.