--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Oct 19 17:28:29 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_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -36232.78 -36309.12
2 -36237.35 -36308.14
--------------------------------------
TOTAL -36233.46 -36308.74
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 5.503480 0.048255 5.079801 5.934562 5.496655 128.86 133.09 1.007
r(A<->C){all} 0.097845 0.000041 0.085322 0.109850 0.097731 382.39 477.21 1.008
r(A<->G){all} 0.386483 0.000189 0.360782 0.413789 0.386391 390.75 395.80 1.001
r(A<->T){all} 0.040035 0.000017 0.032453 0.048534 0.039797 537.30 566.19 1.000
r(C<->G){all} 0.022303 0.000024 0.013116 0.032052 0.022106 538.10 665.83 1.000
r(C<->T){all} 0.413674 0.000180 0.387208 0.439246 0.413907 259.80 372.76 1.000
r(G<->T){all} 0.039659 0.000020 0.031016 0.048410 0.039527 397.72 610.64 1.000
pi(A){all} 0.324217 0.000017 0.316778 0.332562 0.324263 358.76 518.42 1.000
pi(C){all} 0.203941 0.000011 0.197622 0.210482 0.203948 394.12 490.53 1.002
pi(G){all} 0.181372 0.000012 0.174710 0.188055 0.181313 541.02 553.58 1.001
pi(T){all} 0.290470 0.000016 0.282434 0.297932 0.290419 468.97 480.66 1.000
alpha{1,2} 0.150730 0.000023 0.141556 0.160523 0.150568 251.68 252.79 1.003
alpha{3} 5.405496 0.805778 3.874965 7.194352 5.336269 351.13 368.81 1.001
pinvar{all} 0.049975 0.000057 0.034913 0.064716 0.049971 966.88 1049.78 1.001
------------------------------------------------------------------------------------------------------
* 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
