--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Feb 15 20:23:10 WET 2016
codeml.models=
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/Z_B1/Zika-NS3_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_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/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -4928.76 -4983.65
2 -4925.80 -4999.16
--------------------------------------
TOTAL -4926.45 -4998.46
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_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/Z_B1/Zika-NS3_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} 0.901506 0.006976 0.752029 1.075270 0.896525 350.50 411.29 1.000
r(A<->C){all} 0.026667 0.000047 0.014383 0.040585 0.025990 792.07 862.28 1.000
r(A<->G){all} 0.214110 0.000951 0.157108 0.277052 0.211810 474.31 508.75 1.000
r(A<->T){all} 0.020039 0.000055 0.007348 0.034381 0.019252 801.43 809.91 1.000
r(C<->G){all} 0.006180 0.000011 0.000659 0.012935 0.005567 923.77 935.64 1.000
r(C<->T){all} 0.703350 0.001240 0.629551 0.767336 0.704535 426.95 491.19 1.000
r(G<->T){all} 0.029654 0.000068 0.014148 0.045121 0.028958 484.19 620.85 1.001
pi(A){all} 0.281612 0.000095 0.261988 0.299898 0.281564 1039.31 1155.62 1.002
pi(C){all} 0.235732 0.000078 0.219037 0.253901 0.235384 989.04 1113.83 1.001
pi(G){all} 0.278121 0.000096 0.258271 0.296422 0.278118 1133.19 1194.60 1.000
pi(T){all} 0.204535 0.000069 0.188173 0.220951 0.204203 1026.54 1074.38 1.001
alpha{1,2} 0.054845 0.000606 0.002839 0.088994 0.061138 801.42 939.36 1.000
alpha{3} 4.446388 1.165671 2.519597 6.601797 4.328784 1288.67 1292.96 1.000
pinvar{all} 0.364347 0.001165 0.300813 0.432202 0.364895 1046.36 1100.80 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: One dN/dS ratio for branches, -4658.632923
