TreeTimeUnknownError: Unexpected behavior detected with y-values '[]' - When using augur refine

[PepijnTeuling]

This error occured when running augur refine in a snakefile with a conda based Nextstrain environment, the input being 62 bacterial genomes.

Versions:

• conda: 24.9.2
• nextstrain.cli: 8.5.3
• augur: 26.0.0
• treetime: 0.11.4

The Error Message:

treetime.TreeTimeUnknownError: Error: Unexpected behavior detected in multiply function when determining peak of function with y-values '[]'.

If you see this error please let us know by filling an issue at:
https://github.com/neherlab/treetime/issues

ERROR: Error: Unexpected behavior detected in multiply function when determining peak of function with y-values '[]'.

If you see this error please let us know by filling an issue at:
https://github.com/neherlab/treetime/issues

ERROR in TreeTime.run: An error occurred which was not properly handled in TreeTime. If this error persists, please let us know by filing a new issue including the original command and the error above at: https://github.com/neherlab/treetime/issues

ERROR from TreeTime: An error occurred in TreeTime (see above). This may be due to an issue with TreeTime or Augur.
Please report you are calling TreeTime via Augur.

Related Issue

#270
This issue is about the same error (although outside of augur), and I would guess with the same cause as well: the genomes being too long.
In #270 a work-around is suggested, but I am unsure how to go about it programmatically.

Complete Log Files

The complete stdout and stderr from the augur refine step:
refine.stdout.txt
refine.stderr.txt

[rneher]

Hello @PepijnTeuling

To diagnose this issue, it would be useful to know the exact command you ran. Also, if you could share the input data, that would be of great help.

From the stdout, I see two potential problems:

• your tree has very long branches
• there is very little temporal signal

best,
richard

[PepijnTeuling]

Hello @rneher,

I wasn't able to find the treetime command augur uses when augur refine is called, but the augur command I used is:

augur refine --tree tree.nwk --alignment alignment.fasta --metadata metadata.tsv --output-tree tree.refined.nwk --output-node-data branch_lengths.json --timetree --coalescent opt --date-confidence --date-inference marginal 1>refine.stdout.txt 2>refine.stderr.txt

Sadly, I can't share the input data.

However, I've already tried the workflow using a VCF file as input instead, which, if I understand correctly, only uses the sites where every sample has a variant for the alignment, and that did work. Which makes me think you are correct about the branches being too long.

Kind regards,
Pepijn