--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Oct 19 06:58:08 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -35899.70 -35980.58
2 -35902.91 -35973.82
--------------------------------------
TOTAL -35900.36 -35979.88
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 5.452486 0.045794 5.013301 5.859781 5.447291 112.31 201.81 1.002
r(A<->C){all} 0.102391 0.000043 0.090414 0.115923 0.102366 401.51 516.30 1.004
r(A<->G){all} 0.389801 0.000184 0.364947 0.417049 0.389762 265.10 311.11 1.001
r(A<->T){all} 0.037860 0.000016 0.029719 0.045176 0.037770 563.52 578.41 1.000
r(C<->G){all} 0.021078 0.000023 0.011993 0.030535 0.020865 533.55 574.03 1.000
r(C<->T){all} 0.409196 0.000169 0.382165 0.433700 0.409341 339.94 369.63 1.000
r(G<->T){all} 0.039673 0.000021 0.031186 0.048794 0.039631 416.80 489.57 1.001
pi(A){all} 0.323543 0.000018 0.315071 0.331403 0.323600 371.19 447.00 1.000
pi(C){all} 0.203592 0.000011 0.197668 0.210049 0.203561 431.95 468.93 1.000
pi(G){all} 0.180881 0.000011 0.174237 0.186777 0.180910 288.19 378.62 1.001
pi(T){all} 0.291983 0.000016 0.284363 0.299538 0.291714 443.43 509.39 1.000
alpha{1,2} 0.151486 0.000022 0.142927 0.161044 0.151234 445.45 461.96 1.001
alpha{3} 5.219533 0.782123 3.563880 6.973702 5.114155 901.73 1024.86 1.000
pinvar{all} 0.048601 0.000059 0.033711 0.063228 0.048530 994.59 1170.85 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
