How to extract inferred branch lengths?

[leonkt]

I am using the following commands to generate the stan script, and run the stan script respectively:

phylostan build -s sample.stan -m JC69 -C 4 --estimate_rate --clock strict --coalescent constant
phylostan run -s sample.stan -m JC69 -C 4 --estimate_rate --clock strict --coalescent constant -i out.fasta -t sample_newick.newick -o sample -q meanfield

I would expect that there are branch lengths from the bottommost tree in sample.trees, as given below, but, there are none.

I've also tried looking in the file populated in the -o flag of the run command, labelled as VB samples below. I have fewer than 10 sequences, yet there are 10 nonzero branch lengths in the VB samples file, so I am not sure what to make of this. Is there another place that I can get inferred branch lengths? Or is there something I'm doing incorrectly?

Original data
VB samples
Script generated using build
Tree topology
sample.trees

[4ment]

Hi @leonkt -- you can find the branch lengths in terms of expected number of substitutions per site in the sample.txt file. They are labelled blensUnscaled.1, blensUnscaled.2,...,blensUnscaled.10.
Since it is a time tree the branch lengths in samples.trees file should be in unit of time (e.g. years). I said should because there was bug and every branch length was equal to 0. It is fixed now so please use the latest version of phylostan.