raise RuntimeError("Failed to parse newick tree: %s" % RuntimeError: Failed to parse newick tree

[Cholineborzoi]

Hi!

I am trying to learn how to use Cactus, and having problems with the phylogenetic tree. I want to run it for human and dog. How can I make a Newick tree of that?

I had a following one when getting the error in title: ((Human:0.0, Dog:0.052458):0.02)

I formed that from https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/ but I am not sure if that is even correct. Thank you!

[glennhickey]

The Newick format is defined here where it shows that it must end with a semicolon.

[Cholineborzoi]

I tried that with (Human:0.0, Dog:0.052458):0.02; but got a following error:

RuntimeError: Error parsing tree "((Human:0.0,Dog:0.052458)Anc1:0.02)Anc0;": Node Anc0 (parent of Anc1) has single descendant: Please remove all such nodes and try again.

[diekhans]

I would suggest visualizing your tree with FigTree or similar tool to make sure it is valid and what you expected.

While newick simplicity also means it is very easy to get it wrong.

Cholineborzoi @.***> writes:

I tried that with (Human:0.0, Dog:0.052458):0.02; but got a following error:

RuntimeError: Error parsing tree "((Human:0.0,Dog:0.052458)Anc1:0.02)Anc0;": Node Anc0 (parent of Anc1) has single descendant: Please remove all such nodes and try again.

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[glennhickey]

I tried that with (Human:0.0, Dog:0.052458):0.02; but got a following error:

This error is because you are adding a second node above the human/dog ancestor. If you only have two genomes to align, your tree should look like

(Human:0.0, Dog:0.052458);