--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Oct 06 22:59:35 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/DATA/Zika/B3_A/Zika-NS4B_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/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/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3259.86 -3359.88
2 -3271.49 -3357.62
--------------------------------------
TOTAL -3260.56 -3359.29
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/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/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 16.297712 2.385388 13.119120 19.065950 16.292040 293.92 374.73 1.003
r(A<->C){all} 0.024798 0.000071 0.010034 0.042033 0.024099 346.64 388.90 1.001
r(A<->G){all} 0.231548 0.003217 0.113716 0.329417 0.237929 110.39 133.88 1.004
r(A<->T){all} 0.056773 0.000199 0.029493 0.083506 0.055901 324.85 370.05 1.001
r(C<->G){all} 0.010469 0.000030 0.001605 0.021235 0.009555 528.24 542.75 1.000
r(C<->T){all} 0.649993 0.004824 0.535716 0.799492 0.639936 99.48 120.42 1.004
r(G<->T){all} 0.026419 0.000096 0.008932 0.046072 0.025178 143.57 282.29 1.001
pi(A){all} 0.259620 0.000233 0.230796 0.288708 0.259513 844.12 886.73 1.000
pi(C){all} 0.254255 0.000200 0.228274 0.283310 0.254509 761.44 794.63 1.000
pi(G){all} 0.262438 0.000233 0.231487 0.290401 0.262483 587.99 606.32 1.000
pi(T){all} 0.223686 0.000181 0.197806 0.249775 0.223213 693.39 707.42 1.001
alpha{1,2} 0.071008 0.000011 0.064773 0.077572 0.070856 281.06 368.08 1.003
alpha{3} 0.264338 0.000268 0.234235 0.297281 0.263165 722.38 800.07 1.000
pinvar{all} 0.326829 0.002141 0.238028 0.418578 0.328881 207.31 282.37 1.002
------------------------------------------------------------------------------------------------------
* 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 -2716.8929
Model 2: PositiveSelection -2716.8929
Model 0: one-ratio -2738.892858
Model 3: discrete -2716.715815
Model 7: beta -2719.632129
Model 8: beta&w>1 -2719.634455
Model 0 vs 1 43.99991600000067
Model 2 vs 1 0.0
Model 8 vs 7 0.004651999999623513
