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neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
MIT License
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'branch_mutations.txt' output always empty (v 0.11.3) #272

Closed LewisCEMason closed 1 month ago

LewisCEMason commented 4 months ago

Dear Devs,

I hope that you are well.

I am using TreeTime (v 0.11.3), installed with conda install bioconda::treetime.

I am using the ancestral sequence reconstruction (with VCF files) command, treetime ancestral --aln data/tb/lee_2015.vcf.gz --vcf-reference data/tb/tb_ref.fasta --tree data/tb/lee_2015.nwk , (but with my own files) as a means to obtain the branch_mutations.txt output, but am finding that this output is always empty. The other outputs (ancestral_sequences.vcf, annotated_tree.nexus, auspice_tree.json, sequence_evolution_model.txt) are not empty.

I am unsure of what is going on here, and was wondering if you could help?

rneher commented 1 month ago

thanks for alerting us of this. I have found the bug and it should be fixed with the next release.

rneher commented 1 month ago

https://github.com/neherlab/treetime/commit/52d7e9a509ab12e7e088d29975347a2618c047f1