--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Oct 08 21:15:53 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/B2_A/Zika-NS1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/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/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -4274.14 -4360.36
2 -4319.81 -4396.65
--------------------------------------
TOTAL -4274.83 -4395.96
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/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/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 14.238639 2.011118 11.393440 17.073970 14.172340 123.09 343.90 1.070
r(A<->C){all} 0.010970 0.000109 0.000395 0.029331 0.005482 247.52 247.72 3.591
r(A<->G){all} 0.079640 0.006165 0.004784 0.214303 0.058973 90.18 128.89 3.726
r(A<->T){all} 0.013052 0.000141 0.000771 0.033858 0.006762 160.89 180.43 3.465
r(C<->G){all} 0.004127 0.000018 0.000060 0.012472 0.001907 251.66 380.67 2.302
r(C<->T){all} 0.883697 0.011859 0.702386 0.991429 0.902717 87.99 112.25 4.296
r(G<->T){all} 0.008513 0.000066 0.000414 0.023799 0.004256 191.09 251.83 2.778
pi(A){all} 0.292165 0.000175 0.266018 0.318110 0.291963 385.16 553.53 1.008
pi(C){all} 0.214210 0.000132 0.189858 0.234657 0.214215 304.72 655.91 1.056
pi(G){all} 0.291395 0.000180 0.265212 0.317405 0.290804 297.79 546.58 1.016
pi(T){all} 0.202230 0.000118 0.180089 0.223212 0.201853 240.08 553.75 1.040
alpha{1,2} 0.068491 0.000028 0.058976 0.078069 0.068455 340.42 385.08 1.954
alpha{3} 0.404961 0.021970 0.230589 0.595740 0.326821 166.95 256.63 7.642
pinvar{all} 0.314600 0.002943 0.222890 0.421031 0.310498 259.54 442.40 1.978
------------------------------------------------------------------------------------------------------
* 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 -3617.64223
Model 2: PositiveSelection -3617.64223
Model 0: one-ratio -3623.248625
Model 3: discrete -3609.543119
Model 7: beta -3610.243602
Model 8: beta&w>1 -3610.244129
Model 0 vs 1 11.212790000000496
Model 2 vs 1 0.0
Model 8 vs 7 0.0010540000002947636
