clock does not create a text-file with the rate estimate

[1ucyb]

I'm using treetime clock to estimate evolutionary rates for ~300 simulated trees. In the documentation, it says "a text-file with the rate estimate" will be produced. However, the only files I'm getting are:

• outliers.tsv
• rerooted.newick
• root_to_tip_regression.pdf
• rtt.csv

None of which have easy-to-access text with the rate estimate. I'm just using the default settings for clock, but I've also tried with --verbose 6. I'm able to pull the rate from the output stream, but I thought I'd flag it in case it was an oversight! Sorry if I'm missing something - I'm new to treetime.

[ivan-aksamentov]

Hi @1ucyb

Thanks for reporting this!

Fixed in PR #575. Until it's released, you can try the fix as follows:

# one-shot, no install
uvx --from git+https://github.com/neherlab/treetime.git@c78edd1a treetime clock --tree ...

# or install it
pip install git+https://github.com/neherlab/treetime.git@c78edd1a

[ivan-aksamentov]

Fix is released in treetime 0.12.0