Error: unsupported rooting mechanisms or root not found

Help and Getting Started
1

Hello everyone,

I’m new to nextstrain, I was trying to run a division-focused analysis on data downloaded from gisaid. the iqtree algorithm seem to have worked fine for 3 ours; then, augure refine was launched and it gave me this warnings:

WARNING: TreeAnc._attach_sequences_to_nodes: NO SEQUENCE FOR LEAF:
Lu_an/226/2020

WARNING: TreeAnc: 1 nodes don’t have a matching sequence in the
alignment. POSSIBLE ERROR.

Then, it stops abruptly with this

File “/localRaid/anaconda3/envs/nextstrain/lib/python3.6/site-packages/treetime/treetime.py”, line 453, 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 you please help me to complete the analysis?
thank you in advance,
Emanuele

2

Hi @Emanuele, we also noticed this recently due to the sample name Lu'an being renamed to Lu_an. I believe we’ve fixed this in our curation scripts – could you try re-downloading the “nextmeta” and “nextfasta” from GISAID and rerunning?

3

Hi @james,

actually I figured out Lu’an samples were causing troubles and I’ve overcome the error by just dropping the samples from the datasets and it worked.

Thank you for your reply,
Emanuele