--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Oct 19 02:08:22 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/Ebola_B1/LC_2/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_2/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/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -35955.53 -36026.21 2 -35953.66 -36031.70 -------------------------------------- TOTAL -35954.21 -36031.01 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_2/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/Ebola_B1/LC_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 5.379831 0.042136 4.997779 5.790492 5.375557 135.69 144.33 1.000 r(A<->C){all} 0.098671 0.000040 0.086464 0.110626 0.098566 557.78 574.05 1.000 r(A<->G){all} 0.379937 0.000180 0.353914 0.405570 0.379896 273.89 330.01 1.008 r(A<->T){all} 0.042365 0.000017 0.034169 0.050134 0.042224 508.25 598.79 1.000 r(C<->G){all} 0.020623 0.000022 0.011639 0.029634 0.020397 646.05 652.63 1.000 r(C<->T){all} 0.419337 0.000168 0.394668 0.444703 0.419491 257.86 318.11 1.014 r(G<->T){all} 0.039067 0.000020 0.030732 0.047850 0.038793 514.03 519.62 1.003 pi(A){all} 0.324266 0.000019 0.315611 0.332364 0.324190 273.55 382.89 1.003 pi(C){all} 0.204597 0.000012 0.197729 0.211020 0.204563 509.25 561.33 1.004 pi(G){all} 0.181073 0.000011 0.174498 0.187413 0.181055 406.70 457.12 1.001 pi(T){all} 0.290064 0.000017 0.281849 0.297978 0.290166 461.98 490.23 1.001 alpha{1,2} 0.151146 0.000022 0.142453 0.160457 0.150914 363.24 422.58 1.001 alpha{3} 5.608932 0.870711 3.925032 7.525801 5.502854 727.49 744.48 1.000 pinvar{all} 0.050245 0.000062 0.034138 0.065285 0.050098 902.88 1047.68 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