--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Oct 19 12:03:19 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -35375.52 -35442.66
2 -35373.86 -35449.38
--------------------------------------
TOTAL -35374.38 -35448.69
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_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} 5.556503 0.050304 5.117634 5.996952 5.551489 163.14 197.44 1.000
r(A<->C){all} 0.099147 0.000046 0.086853 0.113458 0.099014 501.43 506.57 1.000
r(A<->G){all} 0.388909 0.000182 0.360902 0.413095 0.388934 312.86 438.98 1.001
r(A<->T){all} 0.039983 0.000019 0.031427 0.048555 0.039971 382.72 505.53 1.000
r(C<->G){all} 0.020250 0.000026 0.010416 0.030580 0.019965 323.36 535.70 1.003
r(C<->T){all} 0.415851 0.000178 0.389904 0.441827 0.415654 361.68 459.64 1.001
r(G<->T){all} 0.035860 0.000021 0.027399 0.045197 0.035741 430.80 513.24 1.000
pi(A){all} 0.323769 0.000017 0.316176 0.331822 0.323746 385.18 426.10 1.000
pi(C){all} 0.204384 0.000011 0.197566 0.210682 0.204348 473.25 491.17 1.000
pi(G){all} 0.181203 0.000011 0.174470 0.187692 0.181184 521.20 562.12 1.000
pi(T){all} 0.290643 0.000015 0.282312 0.297904 0.290691 543.90 548.24 1.000
alpha{1,2} 0.148007 0.000021 0.138910 0.156704 0.147839 392.42 530.79 1.000
alpha{3} 5.199963 0.733623 3.641152 6.890747 5.115713 759.13 865.93 1.000
pinvar{all} 0.050470 0.000060 0.035978 0.065821 0.050287 1162.81 1199.10 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
