--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Oct 19 12:03:19 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_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -35375.52 -35442.66 2 -35373.86 -35449.38 -------------------------------------- TOTAL -35374.38 -35448.69 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/Ebola_B1/LC_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/LC_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 5.556503 0.050304 5.117634 5.996952 5.551489 163.14 197.44 1.000 r(A<->C){all} 0.099147 0.000046 0.086853 0.113458 0.099014 501.43 506.57 1.000 r(A<->G){all} 0.388909 0.000182 0.360902 0.413095 0.388934 312.86 438.98 1.001 r(A<->T){all} 0.039983 0.000019 0.031427 0.048555 0.039971 382.72 505.53 1.000 r(C<->G){all} 0.020250 0.000026 0.010416 0.030580 0.019965 323.36 535.70 1.003 r(C<->T){all} 0.415851 0.000178 0.389904 0.441827 0.415654 361.68 459.64 1.001 r(G<->T){all} 0.035860 0.000021 0.027399 0.045197 0.035741 430.80 513.24 1.000 pi(A){all} 0.323769 0.000017 0.316176 0.331822 0.323746 385.18 426.10 1.000 pi(C){all} 0.204384 0.000011 0.197566 0.210682 0.204348 473.25 491.17 1.000 pi(G){all} 0.181203 0.000011 0.174470 0.187692 0.181184 521.20 562.12 1.000 pi(T){all} 0.290643 0.000015 0.282312 0.297904 0.290691 543.90 548.24 1.000 alpha{1,2} 0.148007 0.000021 0.138910 0.156704 0.147839 392.42 530.79 1.000 alpha{3} 5.199963 0.733623 3.641152 6.890747 5.115713 759.13 865.93 1.000 pinvar{all} 0.050470 0.000060 0.035978 0.065821 0.050287 1162.81 1199.10 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