--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Feb 15 21:06:42 WET 2016
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/Z_B1/Zika-NS3_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_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/Z_B1/Zika-NS3_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -5581.66 -5640.86
2 -5585.27 -5645.57
--------------------------------------
TOTAL -5582.33 -5644.89
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_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/Z_B1/Zika-NS3_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} 0.859018 0.003664 0.736074 0.969646 0.856905 695.53 768.38 1.000
r(A<->C){all} 0.029000 0.000048 0.016669 0.042964 0.028771 823.55 903.05 1.000
r(A<->G){all} 0.177361 0.000461 0.137213 0.219652 0.176055 495.81 587.70 1.000
r(A<->T){all} 0.042422 0.000079 0.026008 0.059723 0.041636 624.58 782.46 1.000
r(C<->G){all} 0.010853 0.000021 0.003110 0.020055 0.010425 751.98 789.36 1.000
r(C<->T){all} 0.710044 0.000745 0.659099 0.765096 0.710686 478.75 526.70 1.000
r(G<->T){all} 0.030320 0.000060 0.015788 0.045387 0.029759 819.19 846.48 1.000
pi(A){all} 0.282608 0.000092 0.264149 0.301131 0.282933 917.73 1017.02 1.000
pi(C){all} 0.232417 0.000079 0.216057 0.249589 0.232264 839.75 989.88 1.000
pi(G){all} 0.276809 0.000099 0.257597 0.295299 0.276809 1007.83 1080.16 1.000
pi(T){all} 0.208167 0.000074 0.192694 0.225945 0.208083 1150.21 1190.56 1.000
alpha{1,2} 0.111785 0.000128 0.090365 0.133791 0.111576 1289.34 1293.29 1.000
alpha{3} 4.745324 1.227989 2.839602 7.007891 4.623983 1069.20 1285.10 1.000
pinvar{all} 0.250527 0.001606 0.173561 0.329390 0.252034 1070.58 1210.19 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, -5223.918394
