IQ-TREE multicore version 1.6.8 for Mac OS X 64-bit built Oct 28 2018 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: DJMLabMac.local (AVX2, FMA3, 16 GB RAM) Command: iqtree -s 18s_small.phy -m MFP -mset mrbayes -bb 1000 Seed: 90832 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Apr 5 13:29:06 2019 Kernel: AVX+FMA - 1 threads (8 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 8 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file 18s_small.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 9 sequences with 1710 columns, 122 distinct patterns 56 parsimony-informative, 107 singleton sites, 1547 constant sites Gap/Ambiguity Composition p-value 1 Pontellina_plumata 0.23% passed 99.70% 2 Temora_discaudata 2.28% passed 88.59% 3 Epischura_baikalensis 1.40% passed 99.14% 4 Epischura_chankensis 1.40% passed 99.14% 5 Heterocope_septentrionalis 1.35% passed 99.68% 6 Epischura_fluviatilis 1.46% passed 98.09% 7 Epischura_nevadensis 1.40% passed 98.95% 8 Epischura_nordenskioldi 1.29% passed 97.82% 9 Epischura_lacustris 43.80% passed 52.63% **** TOTAL 6.07% 0 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: Epischura_chankensis is identical to Epischura_baikalensis but kept for subsequent analysis Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds NOTE: ModelFinder requires 0 MB RAM! ModelFinder will test 78 DNA models (sample size: 1710) ... No. Model -LnL df AIC AICc BIC 1 JC 3525.037 15 7080.073 7080.357 7161.737 2 JC+I 3503.938 16 7039.875 7040.196 7126.983 3 JC+G4 3503.933 16 7039.866 7040.187 7126.973 4 JC+I+G4 3503.632 17 7041.265 7041.627 7133.817 5 JC+R2 3504.254 17 7042.507 7042.869 7135.060 6 JC+R3 3503.924 19 7045.848 7046.298 7149.289 14 F81+F 3511.401 18 7058.802 7059.206 7156.798 15 F81+F+I 3490.859 19 7019.717 7020.167 7123.158 16 F81+F+G4 3490.838 19 7019.677 7020.126 7123.117 17 F81+F+I+G4 3490.579 20 7021.158 7021.655 7130.043 18 F81+F+R2 3490.905 20 7021.809 7022.307 7130.694 19 F81+F+R3 3490.696 22 7025.393 7025.992 7145.166 27 K2P 3492.085 16 7016.171 7016.492 7103.279 28 K2P+I 3469.129 17 6972.258 6972.620 7064.810 29 K2P+G4 3469.238 17 6972.475 6972.837 7065.028 30 K2P+I+G4 3468.621 18 6973.243 6973.647 7071.239 31 K2P+R2 3468.754 18 6973.509 6973.913 7071.505 32 K2P+R3 3468.520 20 6977.039 6977.536 7085.924 40 HKY+F 3478.146 19 6994.293 6994.742 7097.733 41 HKY+F+I 3455.344 20 6950.688 6951.185 7059.573 42 HKY+F+G4 3455.435 20 6950.870 6951.367 7059.755 43 HKY+F+I+G4 3454.845 21 6951.690 6952.238 7066.020 44 HKY+F+R2 3454.900 21 6951.800 6952.348 7066.130 45 HKY+F+R3 3454.675 23 6955.349 6956.004 7080.567 53 SYM 3483.093 20 7006.186 7006.684 7115.071 54 SYM+I 3461.061 21 6964.121 6964.669 7078.450 55 SYM+G4 3461.084 21 6964.168 6964.715 7078.497 56 SYM+I+G4 3460.506 22 6965.011 6965.611 7084.785 57 SYM+R2 3460.418 22 6964.836 6965.436 7084.609 58 SYM+R3 3460.227 24 6968.454 6969.166 7099.116 66 GTR+F 3467.728 23 6981.455 6982.110 7106.673 67 GTR+F+I 3446.667 24 6941.335 6942.047 7071.997 68 GTR+F+G4 3446.642 24 6941.284 6941.996 7071.946 69 GTR+F+I+G4 3446.115 25 6942.230 6943.002 7078.336 70 GTR+F+R2 3445.967 25 6941.933 6942.705 7078.040 71 GTR+F+R3 3445.817 27 6945.634 6946.533 7092.629 Akaike Information Criterion: GTR+F+G4 Corrected Akaike Information Criterion: GTR+F+G4 Bayesian Information Criterion: HKY+F+I Best-fit model: HKY+F+I chosen according to BIC All model information printed to 18s_small.phy.model.gz CPU time for ModelFinder: 0.159 seconds (0h:0m:0s) Wall-clock time for ModelFinder: 0.176 seconds (0h:0m:0s) Generating 1000 samples for ultrafast bootstrap (seed: 90832)... NOTE: 0 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) 1. Initial log-likelihood: -3499.897 2. Current log-likelihood: -3478.222 3. Current log-likelihood: -3464.987 4. Current log-likelihood: -3455.792 5. Current log-likelihood: -3455.348 Optimal log-likelihood: -3455.343 Rate parameters: A-C: 1.00000 A-G: 3.74723 A-T: 1.00000 C-G: 1.00000 C-T: 3.74723 G-T: 1.00000 Base frequencies: A: 0.268 C: 0.199 G: 0.257 T: 0.276 Proportion of invariable sites: 0.767 Parameters optimization took 5 rounds (0.003 sec) Computing ML distances based on estimated model parameters... 0.000 sec Computing BIONJ tree... 0.000 seconds Log-likelihood of BIONJ tree: -3449.831 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.026 second Computing log-likelihood of 90 initial trees ... 0.028 seconds Current best score: -3445.475 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -3445.340 UPDATE BEST LOG-LIKELIHOOD: -3445.337 Iteration 10 / LogL: -3445.340 / Time: 0h:0m:0s Iteration 20 / LogL: -3445.341 / Time: 0h:0m:0s Finish initializing candidate tree set (1) Current best tree score: -3445.337 / CPU time: 0.120 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- UPDATE BEST LOG-LIKELIHOOD: -3445.336 UPDATE BEST LOG-LIKELIHOOD: -3445.336 Iteration 30 / LogL: -3445.337 / Time: 0h:0m:0s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -3445.336 Iteration 40 / LogL: -3445.339 / Time: 0h:0m:0s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -3445.335 UPDATE BEST LOG-LIKELIHOOD: -3445.335 UPDATE BEST LOG-LIKELIHOOD: -3445.335 Iteration 50 / LogL: -3445.335 / Time: 0h:0m:0s (0h:0m:0s left) Log-likelihood cutoff on original alignment: -3471.396 Iteration 60 / LogL: -3445.339 / Time: 0h:0m:0s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -3445.335 UPDATE BEST LOG-LIKELIHOOD: -3445.335 UPDATE BEST LOG-LIKELIHOOD: -3445.335 Iteration 70 / LogL: -3445.335 / Time: 0h:0m:0s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -3445.335 Iteration 80 / LogL: -3445.337 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 90 / LogL: -3445.335 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 100 / LogL: -3445.336 / Time: 0h:0m:0s (0h:0m:0s left) Log-likelihood cutoff on original alignment: -3471.706 NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998 TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -3445.335 Optimal log-likelihood: -3445.335 Rate parameters: A-C: 1.00000 A-G: 4.07094 A-T: 1.00000 C-G: 1.00000 C-T: 4.07094 G-T: 1.00000 Base frequencies: A: 0.268 C: 0.199 G: 0.257 T: 0.276 Proportion of invariable sites: 0.770 Parameters optimization took 1 rounds (0.000 sec) BEST SCORE FOUND : -3445.335 Creating bootstrap support values... Split supports printed to NEXUS file 18s_small.phy.splits.nex Total tree length: 0.130 Total number of iterations: 102 CPU time used for tree search: 0.559 sec (0h:0m:0s) Wall-clock time used for tree search: 0.580 sec (0h:0m:0s) Total CPU time used: 0.603 sec (0h:0m:0s) Total wall-clock time used: 0.634 sec (0h:0m:0s) Computing bootstrap consensus tree... Reading input file 18s_small.phy.splits.nex... 9 taxa and 40 splits. Consensus tree written to 18s_small.phy.contree Reading input trees file 18s_small.phy.contree Log-likelihood of consensus tree: -3445.340 Analysis results written to: IQ-TREE report: 18s_small.phy.iqtree Maximum-likelihood tree: 18s_small.phy.treefile Likelihood distances: 18s_small.phy.mldist Ultrafast bootstrap approximation results written to: Split support values: 18s_small.phy.splits.nex Consensus tree: 18s_small.phy.contree Screen log file: 18s_small.phy.log Date and Time: Fri Apr 5 13:29:06 2019