--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu May 03 12:37:24 WEST 2018
codeml.models=
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/DNGB3/NS5_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DNGB3/NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DNGB3/NS5_1/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/DNGB3/NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -20367.91 -20409.11
2 -20369.96 -20418.84
--------------------------------------
TOTAL -20368.48 -20418.14
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DNGB3/NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DNGB3/NS5_1/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/DNGB3/NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 6.947938 0.119275 6.270727 7.621546 6.940277 443.53 450.31 1.003
r(A<->C){all} 0.041561 0.000014 0.034482 0.048514 0.041486 752.87 814.19 1.000
r(A<->G){all} 0.185576 0.000099 0.167504 0.205517 0.185120 362.56 375.03 1.001
r(A<->T){all} 0.044012 0.000020 0.035257 0.052654 0.043892 607.12 756.36 1.004
r(C<->G){all} 0.024335 0.000014 0.017733 0.032285 0.024186 593.53 699.99 1.000
r(C<->T){all} 0.682253 0.000166 0.656038 0.706038 0.682698 356.06 374.44 1.000
r(G<->T){all} 0.022264 0.000017 0.014851 0.030837 0.022049 647.41 718.30 1.000
pi(A){all} 0.359896 0.000043 0.346897 0.372397 0.360104 730.19 751.51 1.000
pi(C){all} 0.224134 0.000031 0.212589 0.234313 0.224091 725.38 738.22 1.000
pi(G){all} 0.235686 0.000037 0.223808 0.247254 0.235537 772.16 777.42 1.002
pi(T){all} 0.180285 0.000023 0.170948 0.189773 0.180151 508.11 612.78 1.000
alpha{1,2} 0.188527 0.000061 0.172768 0.203394 0.188374 1005.07 1007.69 1.000
alpha{3} 6.044479 0.932346 4.170510 7.889688 5.961256 1501.00 1501.00 1.000
pinvar{all} 0.145187 0.000231 0.116380 0.174606 0.144524 1143.53 1183.29 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
Model: One dN/dS ratio for branches, -19422.972821
