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millanek / Dsuite

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
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Error parsing tree when using Fbranch #13

Closed cbrock2 closed 4 years ago

cbrock2 commented 4 years ago

Hi,

I am getting the following error when running the Fbranch command:

command

Build/Dsuite Fbranch kivu_tree kivu_list_dsuite_Fbkivu_tree.txt > fbranch.txt

error

ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((((((A.elegans,(P.graueri,EdwardSpecies)),((((Y.kamiranzovu,(P.paucidens,Micro)),(N.olivaceous,internalNode0X)),Lit_lig_red),(L.occultidens,M.crebidens))),P.vittatus),A.aeneocolor),(P.nyereri,H.squamipinnis)),A.alluaudi);

I am using the exact same tree in newick format I used to run Dtrios and the kivu_list_dsuite_Fbkivu_tree.txt output file does have f_G values. So the tree seems to work when setting up the possible calculations, but fails in this step.

I have tried removing the outgroup, or even running a small subset of the tree but I continue to get the same parsing error.

Any ideas on what I can try? Thanks so much for the terrific package.

Best

Chad

cbrock2 commented 4 years ago

Nevermind, I figured it out

mrml500 commented 4 years ago

Hi Chad, I'm having exactly the same issue, but haven't worked out the source of the problem. Do you remember how you fixed this?

All the best, Mike

josh3397 commented 1 year ago

Nevermind, I figured it out

Hi Chad, Can you please tell how you figured it out, I'm also having the same issue.