--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Oct 19 06:58:08 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -35899.70        -35980.58
2     -35902.91        -35973.82
--------------------------------------
TOTAL   -35900.36        -35979.88
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/LC_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_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/Ebola_B1/LC_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}         5.452486    0.045794    5.013301    5.859781    5.447291    112.31    201.81    1.002
r(A<->C){all}   0.102391    0.000043    0.090414    0.115923    0.102366    401.51    516.30    1.004
r(A<->G){all}   0.389801    0.000184    0.364947    0.417049    0.389762    265.10    311.11    1.001
r(A<->T){all}   0.037860    0.000016    0.029719    0.045176    0.037770    563.52    578.41    1.000
r(C<->G){all}   0.021078    0.000023    0.011993    0.030535    0.020865    533.55    574.03    1.000
r(C<->T){all}   0.409196    0.000169    0.382165    0.433700    0.409341    339.94    369.63    1.000
r(G<->T){all}   0.039673    0.000021    0.031186    0.048794    0.039631    416.80    489.57    1.001
pi(A){all}      0.323543    0.000018    0.315071    0.331403    0.323600    371.19    447.00    1.000
pi(C){all}      0.203592    0.000011    0.197668    0.210049    0.203561    431.95    468.93    1.000
pi(G){all}      0.180881    0.000011    0.174237    0.186777    0.180910    288.19    378.62    1.001
pi(T){all}      0.291983    0.000016    0.284363    0.299538    0.291714    443.43    509.39    1.000
alpha{1,2}      0.151486    0.000022    0.142927    0.161044    0.151234    445.45    461.96    1.001
alpha{3}        5.219533    0.782123    3.563880    6.973702    5.114155    901.73   1024.86    1.000
pinvar{all}     0.048601    0.000059    0.033711    0.063228    0.048530    994.59   1170.85    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