--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 16:16:38 WET 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=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/Ebolaaminoresults/GP/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/GP/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/ADOPS1/Ebolaaminoresults/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -14092.42 -14123.23
2 -14089.05 -14123.77
--------------------------------------
TOTAL -14089.71 -14123.53
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/GP/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/ADOPS1/Ebolaaminoresults/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 6.556911 0.190533 5.714664 7.437620 6.534617 56.49 343.47 1.002
r(A<->C){all} 0.175483 0.000169 0.150908 0.202342 0.175453 858.02 860.55 1.000
r(A<->G){all} 0.278314 0.000264 0.247862 0.311722 0.277955 742.81 771.39 1.000
r(A<->T){all} 0.087037 0.000112 0.067283 0.108576 0.086854 954.65 1052.92 1.000
r(C<->G){all} 0.076519 0.000126 0.055164 0.098790 0.076513 838.06 926.60 1.000
r(C<->T){all} 0.310348 0.000304 0.277631 0.346815 0.310053 681.72 736.42 1.000
r(G<->T){all} 0.072298 0.000114 0.052367 0.093274 0.072291 810.69 925.40 1.000
pi(A){all} 0.307754 0.000039 0.295173 0.319589 0.307803 800.37 848.81 1.000
pi(C){all} 0.266824 0.000036 0.255714 0.278901 0.266733 1011.26 1136.01 1.000
pi(G){all} 0.209175 0.000033 0.198195 0.220306 0.209107 928.43 1020.98 1.000
pi(T){all} 0.216247 0.000033 0.205411 0.227262 0.216328 713.05 815.99 1.000
alpha{1,2} 0.582723 0.001568 0.502582 0.658086 0.581167 742.20 885.62 1.000
alpha{3} 5.782203 1.325823 3.673887 7.970333 5.672538 1184.86 1274.79 1.000
pinvar{all} 0.007578 0.000033 0.000004 0.018646 0.006324 1138.56 1269.48 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 -7544.961843
Model 2: PositiveSelection -7544.961843
Model 0: one-ratio -7673.28242
Model 3: discrete -7505.428345
Model 7: beta -7516.450556
Model 8: beta&w>1 -7516.453822
Model 0 vs 1 256.641153999999
Model 2 vs 1 0.0
Model 8 vs 7 0.006532000001243432
