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NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
http://NBISweden.github.io/MrBayes/
GNU General Public License v3.0
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Cannot specify amino acid substitution rate higher than 1000 #231

Open roomfortwo opened 3 years ago

roomfortwo commented 3 years ago

Hello there, Following the recommendations in the issue #157, I'm trying to write the model MtArt (as follows)

prset applyto=(all) aamodelpr=fixed(gtr) aarevmatpr=fixed(0.20, 0.20, 0.20, 1.00, 4.00, 500.00, 254.00, 36.00, 98.00, 11.00, 0.20, 154.00, 262.00, 0.20, 0.20, 0.20, 0.20, 183.00, 862.00, 0.20, 262.00, 200.00, 0.20, 121.00, 12.00, 81.00, 3.00, 44.00, 0.20, 41.00, 180.00, 0.20, 12.00, 314.00, 15.00, 0.20, 26.00, 2.00, 21.00, 7.00, 63.00, 11.00, 7.00, 3.00, 0.20, 4.00, 2.00, 13.00, 1.00, 79.00, 16.00, 2.00, 1.00, 6.00, 515.00, 0.20, 209.00, 467.00, 2.00, 0.20, 349.00, 106.00, 0.20, 0.20, 3.00, 4.00, 121.00, 5.00, 79.00, 0.20, 312.00, 67.00, 0.20, 56.00, 0.20, 515.00, 885.00, 106.00, 13.00, 5.00, 20.00, 0.20, 184.00, 0.20, 0.20, 1.00, 14.00, 118.00, 263.00, 11.00, 322.00, 49.00, 0.20, 17.00, 0.20, 0.20, 39.00, 8.00, 0.20, 1.00, 0.20, 12.00, 17.00, 5.00, 15.00, 673.00, 3.00, 398.00, 44.00, 664.00, 52.00, 31.00, 226.00, 11.00, 7.00, 8.00, 144.00, 112.00, 36.00, 87.00, 244.00, 0.20, 166.00, 0.20, 183.00, 44.00, 43.00, 0.20, 19.00, 204.00, 48.00, 70.00, 289.00, 14.00, 47.00, 660.00, 0.20, 0.20, 8.00, 0.20, 22.00, 7.00, 11.00, 2.00, 0.20, 0.20, 21.00, 16.00, 71.00, 54.00, 0.20, 2.00, 0.20, 1.00, 4.00, 251.00, 0.20, 72.00, 87.00, 8.00, 9.00, 191.00, 12.00, 20.00, 117.00, 71.00, 792.00, 18.00, 30.00, 46.00, 38.00, 340.00, 0.20, 23.00, 0.20, 350.00, 0.20, 14.00, 3.00, 0.20 1855.00, 85.00, 26.00, 281.00, 52.00, 32.00, 61.00, 544.00, 0.20, 2.00) statefreqpr=fixed(0.054116, 0.018227, 0.039903, 0.020160, 0.009709, 0.018781, 0.024289, 0.068183, 0.024518, 0.092638, 0.148658, 0.021718, 0.061453, 0.088668, 0.041826, 0.091030, 0.049194, 0.029786, 0.039443, 0.057701); lset rates=gamma ngammacat=4; mcmc ngen=10000000 samplefreq=250 printfreq=1000 nchains=8 temp=0.2 savebrlens=yes starttree=random relburnin=yes burninfrac=0.30; set seed=12345; sumt burnin=5000 showtreeprobs=yes; sump burnin=5000; end;

But as opossed to them, I got the following error, 

  Setting model defaults
  Seed (for generating default start values) = 1920826153
  Setting Aamodelpr to Fixed(Gtr) for partition 1
  Setting Aamodelpr to Fixed(Gtr) for partition 2
  Setting Aamodelpr to Fixed(Gtr) for partition 3
  Setting Aamodelpr to Fixed(Gtr) for partition 4
  Setting Aamodelpr to Fixed(Gtr) for partition 5
  Setting Aamodelpr to Fixed(Gtr) for partition 6
  Setting Aamodelpr to Fixed(Gtr) for partition 7
  Setting Aamodelpr to Fixed(Gtr) for partition 8
  Setting Aamodelpr to Fixed(Gtr) for partition 9
  Setting Aamodelpr to Fixed(Gtr) for partition 10
  Setting Aamodelpr to Fixed(Gtr) for partition 11
  Setting Aamodelpr to Fixed(Gtr) for partition 12
  Setting Aamodelpr to Fixed(Gtr) for partition 13
  Rate value cannot be greater than 1000.00
  Error when setting parameter "Aarevmatpr" (2)
  The error occurred when reading char. 1334-1340 on line 685
     in the file 'concat-v2.nex'

Should I round 1855 into 1000? it's the only value above 1000, Cheers, Luis Alfonso.