--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu May 03 17:49:50 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_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/DNGB3/NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DNGB3/NS5_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/DNGB3/NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -19412.71 -19456.20 2 -19412.33 -19455.77 -------------------------------------- TOTAL -19412.50 -19456.01 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/DNGB3/NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DNGB3/NS5_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/DNGB3/NS5_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} 5.297031 0.064043 4.825848 5.795090 5.282866 493.56 592.04 1.001 r(A<->C){all} 0.046392 0.000019 0.037077 0.054498 0.046230 492.32 656.84 1.001 r(A<->G){all} 0.168282 0.000091 0.149628 0.187338 0.168227 538.91 543.15 1.000 r(A<->T){all} 0.057248 0.000027 0.047805 0.068117 0.057126 577.24 585.06 1.000 r(C<->G){all} 0.032049 0.000019 0.024124 0.040523 0.031906 442.26 575.36 1.000 r(C<->T){all} 0.665076 0.000196 0.638890 0.692134 0.665039 311.35 398.79 1.000 r(G<->T){all} 0.030953 0.000024 0.021691 0.040940 0.030732 706.13 808.78 1.000 pi(A){all} 0.351923 0.000048 0.338122 0.365305 0.352199 685.48 738.24 1.000 pi(C){all} 0.220942 0.000033 0.209613 0.232030 0.220824 780.26 785.25 1.000 pi(G){all} 0.246805 0.000042 0.234659 0.260561 0.246739 593.58 639.11 1.000 pi(T){all} 0.180329 0.000026 0.170598 0.190454 0.180238 600.79 715.31 1.000 alpha{1,2} 0.205354 0.000088 0.187054 0.223256 0.204923 1193.03 1243.98 1.000 alpha{3} 4.432837 0.540636 3.055684 5.848915 4.351101 1373.61 1428.62 1.000 pinvar{all} 0.096954 0.000285 0.064990 0.130298 0.096312 1105.59 1134.83 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: One dN/dS ratio for branches, -16995.687176