--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu May 03 17:49:50 WEST 2018
codeml.models=
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/DNGB3/NS5_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DNGB3/NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DNGB3/NS5_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/DNGB3/NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -19412.71 -19456.20
2 -19412.33 -19455.77
--------------------------------------
TOTAL -19412.50 -19456.01
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DNGB3/NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DNGB3/NS5_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/DNGB3/NS5_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} 5.297031 0.064043 4.825848 5.795090 5.282866 493.56 592.04 1.001
r(A<->C){all} 0.046392 0.000019 0.037077 0.054498 0.046230 492.32 656.84 1.001
r(A<->G){all} 0.168282 0.000091 0.149628 0.187338 0.168227 538.91 543.15 1.000
r(A<->T){all} 0.057248 0.000027 0.047805 0.068117 0.057126 577.24 585.06 1.000
r(C<->G){all} 0.032049 0.000019 0.024124 0.040523 0.031906 442.26 575.36 1.000
r(C<->T){all} 0.665076 0.000196 0.638890 0.692134 0.665039 311.35 398.79 1.000
r(G<->T){all} 0.030953 0.000024 0.021691 0.040940 0.030732 706.13 808.78 1.000
pi(A){all} 0.351923 0.000048 0.338122 0.365305 0.352199 685.48 738.24 1.000
pi(C){all} 0.220942 0.000033 0.209613 0.232030 0.220824 780.26 785.25 1.000
pi(G){all} 0.246805 0.000042 0.234659 0.260561 0.246739 593.58 639.11 1.000
pi(T){all} 0.180329 0.000026 0.170598 0.190454 0.180238 600.79 715.31 1.000
alpha{1,2} 0.205354 0.000088 0.187054 0.223256 0.204923 1193.03 1243.98 1.000
alpha{3} 4.432837 0.540636 3.055684 5.848915 4.351101 1373.61 1428.62 1.000
pinvar{all} 0.096954 0.000285 0.064990 0.130298 0.096312 1105.59 1134.83 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
Model: One dN/dS ratio for branches, -16995.687176
