--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 03 20:14:43 WET 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= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS1/Ebolaaminoresults/L/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/L/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/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -37602.28 -37665.08 2 -37601.87 -37664.18 -------------------------------------- TOTAL -37602.05 -37664.73 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/L/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/ADOPS1/Ebolaaminoresults/L/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 5.315020 0.038693 4.934347 5.696775 5.308014 145.30 181.02 1.009 r(A<->C){all} 0.096495 0.000038 0.084257 0.108645 0.096229 335.43 420.83 1.002 r(A<->G){all} 0.388345 0.000155 0.363129 0.412202 0.388431 254.85 352.82 1.000 r(A<->T){all} 0.041479 0.000015 0.033841 0.049062 0.041493 403.44 489.67 1.004 r(C<->G){all} 0.023727 0.000022 0.014944 0.033012 0.023560 637.39 681.26 1.001 r(C<->T){all} 0.406444 0.000147 0.381563 0.429240 0.406695 403.45 420.72 1.004 r(G<->T){all} 0.043511 0.000020 0.034716 0.052064 0.043406 466.39 610.07 1.000 pi(A){all} 0.323704 0.000018 0.315287 0.331888 0.323529 356.72 426.60 1.009 pi(C){all} 0.204338 0.000011 0.198016 0.211208 0.204316 396.03 504.73 1.003 pi(G){all} 0.181207 0.000012 0.174715 0.187567 0.181225 308.64 380.18 1.000 pi(T){all} 0.290751 0.000017 0.283197 0.298691 0.290636 399.31 474.72 1.003 alpha{1,2} 0.157536 0.000025 0.147565 0.167020 0.157460 265.60 298.90 1.006 alpha{3} 5.804344 0.893050 4.043328 7.646287 5.719054 655.19 885.04 1.001 pinvar{all} 0.055222 0.000057 0.040702 0.070132 0.055168 1291.26 1302.73 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