--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Oct 18 21:31:41 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -35451.43 -35527.83
2 -35450.40 -35528.06
--------------------------------------
TOTAL -35450.79 -35527.96
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 5.426734 0.044161 5.017234 5.827827 5.419345 216.60 245.74 1.000
r(A<->C){all} 0.099165 0.000044 0.087053 0.112981 0.099108 608.36 653.21 1.000
r(A<->G){all} 0.388391 0.000189 0.362043 0.416023 0.388254 342.19 356.60 1.001
r(A<->T){all} 0.041476 0.000018 0.033050 0.049648 0.041384 455.15 494.77 1.000
r(C<->G){all} 0.025366 0.000027 0.014882 0.035423 0.025057 520.27 567.20 1.001
r(C<->T){all} 0.408851 0.000177 0.383751 0.435132 0.409164 408.16 414.56 1.000
r(G<->T){all} 0.036752 0.000023 0.027406 0.045981 0.036578 358.31 505.71 1.000
pi(A){all} 0.324556 0.000018 0.316147 0.332436 0.324534 482.50 487.24 1.001
pi(C){all} 0.204000 0.000012 0.197037 0.210379 0.203923 458.95 471.07 1.000
pi(G){all} 0.181382 0.000011 0.175702 0.188727 0.181322 402.01 490.10 1.002
pi(T){all} 0.290061 0.000017 0.282218 0.298438 0.290056 344.50 351.41 1.000
alpha{1,2} 0.150919 0.000020 0.142367 0.160071 0.150862 469.12 569.36 1.000
alpha{3} 5.468162 0.790078 3.952114 7.298978 5.391826 1050.20 1139.96 1.000
pinvar{all} 0.049861 0.000061 0.034397 0.064633 0.049592 1169.00 1194.29 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
