--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Oct 06 22:59:35 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/DATA/Zika/B3_A/Zika-NS4B_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_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/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -3259.86 -3359.88 2 -3271.49 -3357.62 -------------------------------------- TOTAL -3260.56 -3359.29 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_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/DATA/Zika/B3_A/Zika-NS4B_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} 16.297712 2.385388 13.119120 19.065950 16.292040 293.92 374.73 1.003 r(A<->C){all} 0.024798 0.000071 0.010034 0.042033 0.024099 346.64 388.90 1.001 r(A<->G){all} 0.231548 0.003217 0.113716 0.329417 0.237929 110.39 133.88 1.004 r(A<->T){all} 0.056773 0.000199 0.029493 0.083506 0.055901 324.85 370.05 1.001 r(C<->G){all} 0.010469 0.000030 0.001605 0.021235 0.009555 528.24 542.75 1.000 r(C<->T){all} 0.649993 0.004824 0.535716 0.799492 0.639936 99.48 120.42 1.004 r(G<->T){all} 0.026419 0.000096 0.008932 0.046072 0.025178 143.57 282.29 1.001 pi(A){all} 0.259620 0.000233 0.230796 0.288708 0.259513 844.12 886.73 1.000 pi(C){all} 0.254255 0.000200 0.228274 0.283310 0.254509 761.44 794.63 1.000 pi(G){all} 0.262438 0.000233 0.231487 0.290401 0.262483 587.99 606.32 1.000 pi(T){all} 0.223686 0.000181 0.197806 0.249775 0.223213 693.39 707.42 1.001 alpha{1,2} 0.071008 0.000011 0.064773 0.077572 0.070856 281.06 368.08 1.003 alpha{3} 0.264338 0.000268 0.234235 0.297281 0.263165 722.38 800.07 1.000 pinvar{all} 0.326829 0.002141 0.238028 0.418578 0.328881 207.31 282.37 1.002 ------------------------------------------------------------------------------------------------------ * 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 -2716.8929 Model 2: PositiveSelection -2716.8929 Model 0: one-ratio -2738.892858 Model 3: discrete -2716.715815 Model 7: beta -2719.632129 Model 8: beta&w>1 -2719.634455 Model 0 vs 1 43.99991600000067 Model 2 vs 1 0.0 Model 8 vs 7 0.004651999999623513