--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Oct 06 09:55:26 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/DATA/Zika/B3_A/Zika-NS4B_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3502.25 -3612.69
2 -3509.91 -3627.76
--------------------------------------
TOTAL -3502.94 -3627.06
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 13.892731 2.556904 10.971420 17.102380 13.786470 14.31 47.95 1.147
r(A<->C){all} 0.012176 0.000126 0.001041 0.033276 0.005110 4.97 9.11 1.456
r(A<->G){all} 0.100693 0.010644 0.010608 0.277797 0.024105 4.02 7.87 1.503
r(A<->T){all} 0.021531 0.000397 0.002084 0.056989 0.008299 4.58 8.78 1.448
r(C<->G){all} 0.004746 0.000027 0.000003 0.015489 0.002032 7.12 10.60 1.306
r(C<->T){all} 0.852714 0.020393 0.616312 0.980607 0.959244 3.88 7.77 1.512
r(G<->T){all} 0.008139 0.000063 0.000638 0.024472 0.003686 6.79 10.60 1.384
pi(A){all} 0.257153 0.000212 0.229895 0.285269 0.256978 337.02 583.51 1.000
pi(C){all} 0.254620 0.000204 0.226931 0.283140 0.254973 460.86 578.83 1.005
pi(G){all} 0.260478 0.000226 0.232317 0.291663 0.260072 455.76 478.18 1.017
pi(T){all} 0.227749 0.000186 0.202969 0.255321 0.227727 215.02 278.30 1.005
alpha{1,2} 0.072840 0.000017 0.065347 0.081024 0.072772 11.77 55.86 1.105
alpha{3} 0.434918 0.024610 0.261500 0.670959 0.335564 5.77 16.21 1.245
pinvar{all} 0.190342 0.005976 0.016859 0.311045 0.199249 6.88 18.48 1.183
------------------------------------------------------------------------------------------------------
* 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 -2973.91438
Model 2: PositiveSelection -2973.91438
Model 0: one-ratio -3016.220865
Model 3: discrete -2973.800255
Model 7: beta -2978.040516
Model 8: beta&w>1 -2978.042225
Model 0 vs 1 84.61296999999922
Model 2 vs 1 0.0
Model 8 vs 7 0.003418000000237953
