--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 20:14:43 WET 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=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/Ebolaaminoresults/L/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/L/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/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -37602.28 -37665.08
2 -37601.87 -37664.18
--------------------------------------
TOTAL -37602.05 -37664.73
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/L/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/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 5.315020 0.038693 4.934347 5.696775 5.308014 145.30 181.02 1.009
r(A<->C){all} 0.096495 0.000038 0.084257 0.108645 0.096229 335.43 420.83 1.002
r(A<->G){all} 0.388345 0.000155 0.363129 0.412202 0.388431 254.85 352.82 1.000
r(A<->T){all} 0.041479 0.000015 0.033841 0.049062 0.041493 403.44 489.67 1.004
r(C<->G){all} 0.023727 0.000022 0.014944 0.033012 0.023560 637.39 681.26 1.001
r(C<->T){all} 0.406444 0.000147 0.381563 0.429240 0.406695 403.45 420.72 1.004
r(G<->T){all} 0.043511 0.000020 0.034716 0.052064 0.043406 466.39 610.07 1.000
pi(A){all} 0.323704 0.000018 0.315287 0.331888 0.323529 356.72 426.60 1.009
pi(C){all} 0.204338 0.000011 0.198016 0.211208 0.204316 396.03 504.73 1.003
pi(G){all} 0.181207 0.000012 0.174715 0.187567 0.181225 308.64 380.18 1.000
pi(T){all} 0.290751 0.000017 0.283197 0.298691 0.290636 399.31 474.72 1.003
alpha{1,2} 0.157536 0.000025 0.147565 0.167020 0.157460 265.60 298.90 1.006
alpha{3} 5.804344 0.893050 4.043328 7.646287 5.719054 655.19 885.04 1.001
pinvar{all} 0.055222 0.000057 0.040702 0.070132 0.055168 1291.26 1302.73 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
