conflicting requirements for --tree when using comprehensive constraint tree

[Steven Tavis]

Hello,

I am attempting to estimate branch lengths based on a comprehensive constraint tree however I am running into what seems to be mutually incompatible requirements. If I use a random starting tree I get an error telling me that I need a newick tree as an input:

/home/cades/SLT02/programs/ParGenes/pargenes/pargenes_src/../pargenes_binaries/raxml-ng --msa $msa --model JTT+G4 --prefix $prefix --tree rand{1} --seed 1 --threads 1 --evaluate --tree-constraint $constrainttree
ERROR: Please provide a valid Newick file as an argument of --tree option.

However If I start with a newick tree it tells me that this option does not work with a constraint tree:

/home/cades/SLT02/programs/ParGenes/pargenes/pargenes_src/../pargenes_binaries/raxml-ng --msa $msa --model JTT+G4 --prefix $prefix --tree $besttree --seed 1 --threads 1 --evaluate --tree-constraint $constrainttree

RAxML-NG v. 0.9.0 released on 20.05.2019 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

RAxML-NG was called at 10-Jun-2021 16:52:39 as follows:

/home/cades/SLT02/programs/ParGenes/pargenes/pargenes_src/../pargenes_binaries/raxml-ng --msa /home/cades/SLT02/data/corrEvo/SLT01_corrEvoPgenesFirstRun/parse_run/results/PP_5460_faa/PP_5460_faa.raxml.rba --model JTT+G4 --prefix /home/cades/SLT02/data/corrEvo/SLT01_corrEvoPgenesFixedTopology/PP_5460_faa/PP_5460_faa --tree /home/cades/SLT02/data/corrEvo/SLT01_corrEvoPgenesFirstRun/mlsearch_run/results/PP_5460_faa/PP_5460_faa.raxml.bestTree --seed 1 --threads 1 --evaluate --tree-constraint /home/cades/SLT02/data/corrEvo/SLT01_corrEvoPgenesFixedTopology/PP_5460_faa/PP_5460_faa_constriant.newick

Analysis options:
  run mode: Evaluate tree likelihood
  start tree(s): user
  topological constraint: /home/cades/SLT02/data/corrEvo/SLT01_corrEvoPgenesFixedTopology/PP_5460_faa/PP_5460_faa_constriant.newick
  random seed: 1
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: NONE/sequential


ERROR:  User and parsimony starting trees are not supported in combination with constrained tree inference.
       Please use random starting trees instead.

Both commands work if I remove the --evaluate and --tree-constraint $constrainttree options. Is there a way I can fix this?

Thanks for your help,
SLT

[Alexey Kozlov]

Hi Steven,

raxml-ng can estimate branch lengths on binary trees only. So if your constraint tree contains
multifurcations, you will have to run constrained tree search instead of calling --evaluate.

Best,
Alexey

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[Steven Tavis]

Hi Alexi,

Thank you.

Steven