--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Oct 19 17:28:29 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_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -36232.78        -36309.12
2     -36237.35        -36308.14
--------------------------------------
TOTAL   -36233.46        -36308.74
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_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}         5.503480    0.048255    5.079801    5.934562    5.496655    128.86    133.09    1.007
r(A<->C){all}   0.097845    0.000041    0.085322    0.109850    0.097731    382.39    477.21    1.008
r(A<->G){all}   0.386483    0.000189    0.360782    0.413789    0.386391    390.75    395.80    1.001
r(A<->T){all}   0.040035    0.000017    0.032453    0.048534    0.039797    537.30    566.19    1.000
r(C<->G){all}   0.022303    0.000024    0.013116    0.032052    0.022106    538.10    665.83    1.000
r(C<->T){all}   0.413674    0.000180    0.387208    0.439246    0.413907    259.80    372.76    1.000
r(G<->T){all}   0.039659    0.000020    0.031016    0.048410    0.039527    397.72    610.64    1.000
pi(A){all}      0.324217    0.000017    0.316778    0.332562    0.324263    358.76    518.42    1.000
pi(C){all}      0.203941    0.000011    0.197622    0.210482    0.203948    394.12    490.53    1.002
pi(G){all}      0.181372    0.000012    0.174710    0.188055    0.181313    541.02    553.58    1.001
pi(T){all}      0.290470    0.000016    0.282434    0.297932    0.290419    468.97    480.66    1.000
alpha{1,2}      0.150730    0.000023    0.141556    0.160523    0.150568    251.68    252.79    1.003
alpha{3}        5.405496    0.805778    3.874965    7.194352    5.336269    351.13    368.81    1.001
pinvar{all}     0.049975    0.000057    0.034913    0.064716    0.049971    966.88   1049.78    1.001
------------------------------------------------------------------------------------------------------
* 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