--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Oct 07 10:06:18 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_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3440.23 -3531.67
2 -3427.91 -3537.37
--------------------------------------
TOTAL -3428.60 -3536.68
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 14.463763 3.367703 11.043170 18.079690 14.431530 36.11 220.50 1.318
r(A<->C){all} 0.014426 0.000123 0.000911 0.033546 0.014934 8.56 152.09 1.812
r(A<->G){all} 0.138885 0.012118 0.006894 0.297569 0.166220 8.11 44.22 2.249
r(A<->T){all} 0.034723 0.000617 0.002916 0.072461 0.040509 8.11 245.54 2.058
r(C<->G){all} 0.006844 0.000044 0.000005 0.019511 0.005562 9.55 269.35 1.539
r(C<->T){all} 0.785889 0.025684 0.568984 0.983941 0.729624 7.89 44.87 2.415
r(G<->T){all} 0.019233 0.000222 0.001005 0.044535 0.019667 9.58 254.20 1.910
pi(A){all} 0.258666 0.000240 0.230279 0.291155 0.258204 174.88 479.25 1.020
pi(C){all} 0.254453 0.000203 0.226481 0.281439 0.254350 168.19 551.45 1.015
pi(G){all} 0.260562 0.000236 0.229451 0.290288 0.260112 255.94 467.28 1.000
pi(T){all} 0.226318 0.000192 0.199115 0.253216 0.226236 149.61 478.51 1.000
alpha{1,2} 0.073364 0.000018 0.064645 0.081345 0.073445 31.15 285.15 1.143
alpha{3} 0.359665 0.014423 0.240636 0.600695 0.297884 21.22 301.76 1.633
pinvar{all} 0.237046 0.007041 0.063674 0.374678 0.249203 19.97 112.20 1.682
------------------------------------------------------------------------------------------------------
* 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 -2931.977441
Model 2: PositiveSelection -2931.977339
Model 0: one-ratio -2968.77852
Model 3: discrete -2931.933343
Model 7: beta -2935.281734
Model 8: beta&w>1 -2935.283846
Model 0 vs 1 73.60215799999969
Model 2 vs 1 2.0399999993969686E-4
Model 8 vs 7 0.004223999999339867
