--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Oct 08 21:15:53 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/B2_A/Zika-NS1_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/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/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4274.14 -4360.36 2 -4319.81 -4396.65 -------------------------------------- TOTAL -4274.83 -4395.96 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/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/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 14.238639 2.011118 11.393440 17.073970 14.172340 123.09 343.90 1.070 r(A<->C){all} 0.010970 0.000109 0.000395 0.029331 0.005482 247.52 247.72 3.591 r(A<->G){all} 0.079640 0.006165 0.004784 0.214303 0.058973 90.18 128.89 3.726 r(A<->T){all} 0.013052 0.000141 0.000771 0.033858 0.006762 160.89 180.43 3.465 r(C<->G){all} 0.004127 0.000018 0.000060 0.012472 0.001907 251.66 380.67 2.302 r(C<->T){all} 0.883697 0.011859 0.702386 0.991429 0.902717 87.99 112.25 4.296 r(G<->T){all} 0.008513 0.000066 0.000414 0.023799 0.004256 191.09 251.83 2.778 pi(A){all} 0.292165 0.000175 0.266018 0.318110 0.291963 385.16 553.53 1.008 pi(C){all} 0.214210 0.000132 0.189858 0.234657 0.214215 304.72 655.91 1.056 pi(G){all} 0.291395 0.000180 0.265212 0.317405 0.290804 297.79 546.58 1.016 pi(T){all} 0.202230 0.000118 0.180089 0.223212 0.201853 240.08 553.75 1.040 alpha{1,2} 0.068491 0.000028 0.058976 0.078069 0.068455 340.42 385.08 1.954 alpha{3} 0.404961 0.021970 0.230589 0.595740 0.326821 166.95 256.63 7.642 pinvar{all} 0.314600 0.002943 0.222890 0.421031 0.310498 259.54 442.40 1.978 ------------------------------------------------------------------------------------------------------ * 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 -3617.64223 Model 2: PositiveSelection -3617.64223 Model 0: one-ratio -3623.248625 Model 3: discrete -3609.543119 Model 7: beta -3610.243602 Model 8: beta&w>1 -3610.244129 Model 0 vs 1 11.212790000000496 Model 2 vs 1 0.0 Model 8 vs 7 0.0010540000002947636