--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Oct 19 02:08:22 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_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -35955.53        -36026.21
2     -35953.66        -36031.70
--------------------------------------
TOTAL   -35954.21        -36031.01
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         5.379831    0.042136    4.997779    5.790492    5.375557    135.69    144.33    1.000
r(A<->C){all}   0.098671    0.000040    0.086464    0.110626    0.098566    557.78    574.05    1.000
r(A<->G){all}   0.379937    0.000180    0.353914    0.405570    0.379896    273.89    330.01    1.008
r(A<->T){all}   0.042365    0.000017    0.034169    0.050134    0.042224    508.25    598.79    1.000
r(C<->G){all}   0.020623    0.000022    0.011639    0.029634    0.020397    646.05    652.63    1.000
r(C<->T){all}   0.419337    0.000168    0.394668    0.444703    0.419491    257.86    318.11    1.014
r(G<->T){all}   0.039067    0.000020    0.030732    0.047850    0.038793    514.03    519.62    1.003
pi(A){all}      0.324266    0.000019    0.315611    0.332364    0.324190    273.55    382.89    1.003
pi(C){all}      0.204597    0.000012    0.197729    0.211020    0.204563    509.25    561.33    1.004
pi(G){all}      0.181073    0.000011    0.174498    0.187413    0.181055    406.70    457.12    1.001
pi(T){all}      0.290064    0.000017    0.281849    0.297978    0.290166    461.98    490.23    1.001
alpha{1,2}      0.151146    0.000022    0.142453    0.160457    0.150914    363.24    422.58    1.001
alpha{3}        5.608932    0.870711    3.925032    7.525801    5.502854    727.49    744.48    1.000
pinvar{all}     0.050245    0.000062    0.034138    0.065285    0.050098    902.88   1047.68    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