--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Jan 23 14:58:34 GMT 2020
codeml.models=0 1 2 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=/opt/mrbayes_3.2.2/src
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/data/11res/rplX/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/data/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/11res/rplX/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 /data/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -431.04 -434.12
2 -431.05 -434.74
--------------------------------------
TOTAL -431.05 -434.48
--------------------------------------
Model parameter summaries over the runs sampled in files
"/data/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/11res/rplX/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 "/data/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.896429 0.090892 0.357445 1.494586 0.860553 1311.15 1406.07 1.000
r(A<->C){all} 0.167134 0.019857 0.000001 0.452945 0.128984 108.55 150.92 1.000
r(A<->G){all} 0.166594 0.019803 0.000026 0.457625 0.127979 160.09 204.21 1.001
r(A<->T){all} 0.165910 0.020053 0.000134 0.458103 0.128648 135.20 160.49 1.001
r(C<->G){all} 0.164438 0.020192 0.000075 0.458443 0.125735 186.93 200.46 1.000
r(C<->T){all} 0.165173 0.018522 0.000008 0.427901 0.129134 195.63 206.64 1.002
r(G<->T){all} 0.170750 0.019709 0.000027 0.445923 0.136580 244.13 269.52 1.006
pi(A){all} 0.263564 0.000630 0.214421 0.312594 0.262972 1276.50 1290.98 1.000
pi(C){all} 0.263014 0.000591 0.216419 0.310420 0.263317 1218.98 1309.75 1.000
pi(G){all} 0.307586 0.000629 0.260520 0.357932 0.307057 1161.78 1246.99 1.000
pi(T){all} 0.165836 0.000440 0.125786 0.206985 0.164949 1149.02 1176.22 1.000
alpha{1,2} 0.411714 0.218664 0.000197 1.341564 0.243621 1164.66 1269.92 1.000
alpha{3} 0.448791 0.229546 0.000306 1.401306 0.290476 1175.96 1318.68 1.001
pinvar{all} 0.994907 0.000038 0.983191 0.999998 0.996870 1328.33 1350.36 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
Model 1: NearlyNeutral -406.399605
Model 2: PositiveSelection -406.39957
Model 0: one-ratio -406.399599
Model 7: beta -406.399695
Model 8: beta&w>1 -406.39957
Model 0 vs 1 1.1999999969702912E-5
Model 2 vs 1 7.000000005064066E-5
Model 8 vs 7 2.500000000509317E-4
