--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Oct 19 02:08:22 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/Ebola_B1/LC_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -35955.53 -36026.21
2 -35953.66 -36031.70
--------------------------------------
TOTAL -35954.21 -36031.01
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_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} 5.379831 0.042136 4.997779 5.790492 5.375557 135.69 144.33 1.000
r(A<->C){all} 0.098671 0.000040 0.086464 0.110626 0.098566 557.78 574.05 1.000
r(A<->G){all} 0.379937 0.000180 0.353914 0.405570 0.379896 273.89 330.01 1.008
r(A<->T){all} 0.042365 0.000017 0.034169 0.050134 0.042224 508.25 598.79 1.000
r(C<->G){all} 0.020623 0.000022 0.011639 0.029634 0.020397 646.05 652.63 1.000
r(C<->T){all} 0.419337 0.000168 0.394668 0.444703 0.419491 257.86 318.11 1.014
r(G<->T){all} 0.039067 0.000020 0.030732 0.047850 0.038793 514.03 519.62 1.003
pi(A){all} 0.324266 0.000019 0.315611 0.332364 0.324190 273.55 382.89 1.003
pi(C){all} 0.204597 0.000012 0.197729 0.211020 0.204563 509.25 561.33 1.004
pi(G){all} 0.181073 0.000011 0.174498 0.187413 0.181055 406.70 457.12 1.001
pi(T){all} 0.290064 0.000017 0.281849 0.297978 0.290166 461.98 490.23 1.001
alpha{1,2} 0.151146 0.000022 0.142453 0.160457 0.150914 363.24 422.58 1.001
alpha{3} 5.608932 0.870711 3.925032 7.525801 5.502854 727.49 744.48 1.000
pinvar{all} 0.050245 0.000062 0.034138 0.065285 0.050098 902.88 1047.68 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
