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sample not incorporated #15

Open AndreaAguadoM opened 1 month ago

AndreaAguadoM commented 1 month ago

Hello! My name is Andrea, and I am a bioinformatician from Spain. Lately, I have been working with Usher, but with my latest sample, it seems that the process of incorporation into the tree is "not working". My sample is present in the .pb file but not in the .nh final tree. Also, the sample only appears in the .pb file. Let's say my sample is sample. In the .pb file, it only appears in:

^Znode_24_condensed_2_leaves^R^Hsample22^R sample21^Z2,

while when looking for node_24_condensed_2_leaves in the same file tree, the only thing I can find is (node_24_condensed_2_leaves:0.00259932). I do not understand why my target sample does not get added to the tree (actually, neither of both gets added).

Thanks in advance!

AngieHinrichs commented 4 weeks ago

Hi @AndreaAguadoM! Try adding the --write-uncondensed-final-tree option (-u) when you run usher-sampled. It will create the file uncondensed-final-tree.nh which has all the actual sample names instead of the condensed-node names. (What you see in the .pb file is a mapping of node_24_condensed_2_leaves to sample22 and sample21; the condensed node will be expanded in uncondensed-final-tree.nh.) Please let us know if that doesn't produce the expected result.

AndreaAguadoM commented 4 weeks ago

Thanks a lot!! it solved my problem