--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Oct 19 12:03:19 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -35375.52        -35442.66
2     -35373.86        -35449.38
--------------------------------------
TOTAL   -35374.38        -35448.69
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         5.556503    0.050304    5.117634    5.996952    5.551489    163.14    197.44    1.000
r(A<->C){all}   0.099147    0.000046    0.086853    0.113458    0.099014    501.43    506.57    1.000
r(A<->G){all}   0.388909    0.000182    0.360902    0.413095    0.388934    312.86    438.98    1.001
r(A<->T){all}   0.039983    0.000019    0.031427    0.048555    0.039971    382.72    505.53    1.000
r(C<->G){all}   0.020250    0.000026    0.010416    0.030580    0.019965    323.36    535.70    1.003
r(C<->T){all}   0.415851    0.000178    0.389904    0.441827    0.415654    361.68    459.64    1.001
r(G<->T){all}   0.035860    0.000021    0.027399    0.045197    0.035741    430.80    513.24    1.000
pi(A){all}      0.323769    0.000017    0.316176    0.331822    0.323746    385.18    426.10    1.000
pi(C){all}      0.204384    0.000011    0.197566    0.210682    0.204348    473.25    491.17    1.000
pi(G){all}      0.181203    0.000011    0.174470    0.187692    0.181184    521.20    562.12    1.000
pi(T){all}      0.290643    0.000015    0.282312    0.297904    0.290691    543.90    548.24    1.000
alpha{1,2}      0.148007    0.000021    0.138910    0.156704    0.147839    392.42    530.79    1.000
alpha{3}        5.199963    0.733623    3.641152    6.890747    5.115713    759.13    865.93    1.000
pinvar{all}     0.050470    0.000060    0.035978    0.065821    0.050287   1162.81   1199.10    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