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