--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Oct 28 01:33:26 WEST 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/Ebola_B1_2/VP35/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)
(Values are saved to the file /opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -5986.58 -6035.36
2 -5984.66 -6041.34
--------------------------------------
TOTAL -5985.21 -6040.65
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.707892 0.117704 4.060654 5.374117 4.689819 502.21 503.12 1.000
r(A<->C){all} 0.099672 0.000201 0.071524 0.126818 0.099985 660.12 688.56 1.005
r(A<->G){all} 0.371602 0.000773 0.319848 0.428399 0.371649 553.06 575.13 1.000
r(A<->T){all} 0.061980 0.000146 0.039599 0.085469 0.061478 709.26 795.35 1.001
r(C<->G){all} 0.017052 0.000094 0.000294 0.035115 0.015727 507.82 639.35 1.000
r(C<->T){all} 0.395110 0.000789 0.340850 0.451802 0.394999 548.52 610.03 1.000
r(G<->T){all} 0.054585 0.000163 0.032310 0.081650 0.053617 844.91 904.77 1.000
pi(A){all} 0.329473 0.000108 0.307806 0.348527 0.329738 921.82 971.30 1.000
pi(C){all} 0.230478 0.000090 0.211171 0.248031 0.230472 829.75 875.68 1.001
pi(G){all} 0.200144 0.000078 0.183041 0.216889 0.199955 792.45 904.68 1.000
pi(T){all} 0.239906 0.000088 0.220156 0.257330 0.239858 970.15 984.12 1.001
alpha{1,2} 0.216163 0.000293 0.183874 0.250899 0.214944 944.53 1061.89 1.000
alpha{3} 4.642660 1.034646 2.831330 6.676976 4.537871 1069.81 1285.40 1.000
pinvar{all} 0.018494 0.000168 0.000015 0.042420 0.016337 970.00 1114.27 1.000
------------------------------------------------------------------------------------------------------
* 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 conformat to Simple
--- CODEML SUMMARY
Model 1: NearlyNeutral -5315.861443
Model 2: PositiveSelection -5315.861443
Model 0: one-ratio -5437.423663
Model 3: discrete -5271.931481
Model 7: beta -5273.135006
Model 8: beta&w>1 -5273.135134
Model 0 vs 1 243.1244399999996
Model 2 vs 1 0.0
Model 8 vs 7 2.5599999935366213E-4
