Error in command "Translate" MrBayes ver. 3.2.7

[starsareintherose]

Ctrl-C detected Do you really want to stop the run (y/n)?y Mcmc run aborted Summarizing parameters in files 6.nexus.run1.p and 6.nexus.run2.p Writing summary statistics to file 6.nexus.pstat Using relative burnin ('relburnin=yes'), discarding the first 25 % of samples

  Below are rough plots of the generation (x-axis) versus the log
  probability of observing the data (y-axis). You can use these
  graphs to determine what the burn in for your analysis should be.
  When the log probability starts to plateau you may be at station-
  arity. Sample trees and parameters after the log probability
  plateaus. Of course, this is not a guarantee that you are at sta-
  tionarity. Also examine the convergence diagnostics provided by
  the 'sump' and 'sumt' commands for all the parameters in your
  model. Remember that the burn in is the number of samples to dis-
  card. There are a total of ngen / samplefreq samples taken during
  a MCMC analysis.

  Overlay plot for both runs:
  (1 = Run number 1; 2 = Run number 2; * = Both runs)

  +------------------------------------------------------------+ -2256.79
  |                                   2222222 21************1**|
  |                            2222222  11111*12            2  |
  |                        ****111111111                       |
  |               11*******                                    |
  |          11***22                                           |
  |        2*22                                                |
  |       2                                                    |
  |     22 1                                                   |
  |  222111                                                    |
  |22 11                                                       |
  |  1                                                         |
  |                                                            |
  | 1                                                          |
  |                                                            |
  |1                                                           |
  +------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ -3177.67
  ^                                                            ^
  2000                                                         8200

  Overwriting file "6.nexus.lstat"

  Estimated marginal likelihoods for runs sampled in files
     "6.nexus.run1.p" and "6.nexus.run2.p":
     (Use the harmonic mean for Bayes factor comparisons of models)

     (Values are saved to the file 6.nexus.lstat)

  Run   Arithmetic mean   Harmonic mean
  --------------------------------------
    1      -2260.91         -3251.22
    2      -2282.04         -2875.90
  --------------------------------------
  TOTAL    -2261.61         -3250.52
  --------------------------------------


  Model parameter summaries over the runs sampled in files
     "6.nexus.run1.p" and "6.nexus.run2.p":
     Summaries are based on a total of 126 samples from 2 runs.
     Each run produced 83 samples of which 63 samples were included.
     Parameter summaries saved to file "6.nexus.pstat".
  Overwriting file "6.nexus.pstat"

                                        95% HPD Interval
                                      --------------------
  Parameter      Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
  --------------------------------------------------------------------------------------------------
  TL          0.570267    0.005134    0.470660    0.674830    0.556802      8.81      9.80    0.993
  kappa       2.542388    0.106135    2.064617    3.276662    2.591936     16.61     22.33    1.030
  pi(A)       0.197514    0.000216    0.173883    0.228542    0.197817     11.23     11.86    1.036
  pi(C)       0.265622    0.000219    0.240772    0.294884    0.266540     19.12     19.79    0.992
  pi(G)       0.302154    0.000382    0.268424    0.334160    0.301808      9.53     11.77    1.036
  pi(T)       0.234710    0.000222    0.205301    0.257996    0.235685     20.45     23.57    0.996
  alpha       0.856071    0.095957    0.428223    1.535794    0.787214      4.16      5.11    0.994
  --------------------------------------------------------------------------------------------------
  * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
    correspond to minimal and average ESS among runs.
    ESS value below 100 may indicate that the parameter is undersampled.
  + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
    and Rubin, 1992) should approach 1.0 as runs converge.

Setting sumt contype to Allcompat Setting urn-in to 5000 Summarizing trees in files "6.nexus.run1.t" and "6.nexus.run2.t" Using relative burnin ('relburnin=yes'), discarding the first 25 % of sampled trees Writing statistics to files 6.nexus.<parts|tstat|vstat|trprobs|con> Examining first file ... Found one tree block in file "6.nexus.run1.t" with 83 trees in last block Expecting the same number of trees in the last tree block of all files

Tree reading status:

0 10 20 30 40 50 60 70 80 90 100 v-------v-------v-------v-------v-------v-------v-------v-------v-------v-------v

• Expecting '; or ,' Instead found 'AB481029.1_Camaena_sakishimana' in command 'Translate' Error in command "Translate" The error occurred when reading char. -9335526--9335497 on line 97 in the file '6.nexus'

Returning execution to command line ...

Error in command "Execute"

My file The first line is the 91 lines in the file begin mrbayes; lset nst=2 rates=gamma; Prset statefreqpr=dirichlet(1,1,1,1); mcmcp savebrlens=yes ngen=2000000 samplefreq=100 nchains=4; mcmc; sump; sumt contype=allcompat burnin=5000; end;

[zhangchicool]

It is likely that the trees stored in the .t files are corrupted and incomplete. You can open the .t files with a text editor to examine the content. It is unclear though why this happened.