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 ITS2_small.phy -m MFP -mset mrbayes -bb 1000 Seed: 311576 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Apr 5 13:30:19 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 ITS2_small.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 8 sequences with 267 columns, 155 distinct patterns 70 parsimony-informative, 81 singleton sites, 116 constant sites Gap/Ambiguity Composition p-value 1 Temora_discaudata 11.24% passed 44.68% 2 Pontellina_plumata 17.23% passed 85.10% 3 Heterocope_septentrionalis 11.61% passed 75.53% 4 Epischura_baikalensis 10.11% passed 84.65% 5 Epischura_chankensis 17.23% passed 93.65% 6 Epischura_fluviatilis 9.36% passed 96.00% 7 Epischura_lacustris 5.62% passed 95.60% 8 Epischura_nevadensis 5.99% passed 92.67% **** TOTAL 11.05% 0 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds NOTE: ModelFinder requires 1 MB RAM! ModelFinder will test 78 DNA models (sample size: 267) ... No. Model -LnL df AIC AICc BIC 1 JC 1279.127 13 2584.253 2585.692 2630.887 2 JC+I 1270.190 14 2568.380 2570.047 2618.601 3 JC+G4 1269.604 14 2567.207 2568.874 2617.429 4 JC+I+G4 1269.704 15 2569.407 2571.320 2623.216 5 JC+R2 1269.771 15 2569.541 2571.454 2623.350 6 JC+R3 1269.647 17 2573.293 2575.751 2634.277 14 F81+F 1271.802 16 2575.603 2577.779 2632.999 15 F81+F+I 1262.912 17 2559.823 2562.281 2620.806 16 F81+F+G4 1262.234 17 2558.468 2560.926 2619.452 17 F81+F+I+G4 1262.351 18 2560.701 2563.459 2625.272 18 F81+F+R2 1262.427 18 2560.854 2563.612 2625.425 19 F81+F+R3 1262.287 20 2564.574 2567.989 2636.319 27 K2P 1258.759 14 2545.518 2547.184 2595.739 28 K2P+I 1248.052 15 2526.105 2528.017 2579.913 29 K2P+G4 1248.253 15 2526.506 2528.418 2580.315 30 K2P+I+G4 1247.724 16 2527.448 2529.624 2584.844 31 K2P+R2 1248.408 16 2528.815 2530.991 2586.211 32 K2P+R3 1248.139 18 2532.278 2535.036 2596.848 40 HKY+F 1250.864 17 2535.728 2538.186 2596.711 41 HKY+F+I 1241.592 18 2519.185 2521.943 2583.755 42 HKY+F+G4 1241.408 18 2518.817 2521.575 2583.387 43 HKY+F+I+G4 1241.131 19 2520.261 2523.338 2588.419 44 HKY+F+R2 1241.698 19 2521.395 2524.472 2589.553 45 HKY+F+R3 1241.386 21 2524.772 2528.544 2600.105 53 SYM 1250.125 18 2536.250 2539.008 2600.821 54 SYM+I 1240.864 19 2519.728 2522.805 2587.885 55 SYM+G4 1240.832 19 2519.663 2522.740 2587.821 56 SYM+I+G4 1240.431 20 2520.863 2524.278 2592.608 57 SYM+R2 1241.097 20 2522.195 2525.610 2593.940 58 SYM+R3 1240.749 22 2525.498 2529.645 2604.417 66 GTR+F 1240.559 21 2523.118 2526.889 2598.450 67 GTR+F+I 1231.996 22 2507.992 2512.139 2586.911 68 GTR+F+G4 1231.197 22 2506.394 2510.541 2585.313 69 GTR+F+I+G4 1231.207 23 2508.414 2512.957 2590.921 70 GTR+F+R2 1231.720 23 2509.440 2513.983 2591.947 71 GTR+F+R3 1231.322 25 2512.644 2518.038 2602.325 Akaike Information Criterion: GTR+F+G4 Corrected Akaike Information Criterion: GTR+F+G4 Bayesian Information Criterion: K2P+I Best-fit model: K2P+I chosen according to BIC All model information printed to ITS2_small.phy.model.gz CPU time for ModelFinder: 0.079 seconds (0h:0m:0s) Wall-clock time for ModelFinder: 0.089 seconds (0h:0m:0s) Generating 1000 samples for ultrafast bootstrap (seed: 311576)... NOTE: 0 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) 1. Initial log-likelihood: -1270.762 2. Current log-likelihood: -1248.371 3. Current log-likelihood: -1248.055 Optimal log-likelihood: -1248.052 Rate parameters: A-C: 1.00000 A-G: 2.96438 A-T: 1.00000 C-G: 1.00000 C-T: 2.96438 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.261 Parameters optimization took 3 rounds (0.002 sec) Computing ML distances based on estimated model parameters... 0.000 sec Computing BIONJ tree... 0.000 seconds Log-likelihood of BIONJ tree: -1248.052 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 99 parsimony trees... 0.023 second Computing log-likelihood of 50 initial trees ... 0.015 seconds Current best score: -1247.828 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -1247.773 Iteration 10 / LogL: -1247.816 / Time: 0h:0m:0s Iteration 20 / LogL: -1247.818 / Time: 0h:0m:0s Finish initializing candidate tree set (2) Current best tree score: -1247.773 / CPU time: 0.101 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- UPDATE BEST LOG-LIKELIHOOD: -1247.772 Iteration 30 / LogL: -1247.800 / Time: 0h:0m:0s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -1247.772 Iteration 40 / LogL: -1247.887 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 50 / LogL: -1247.798 / Time: 0h:0m:0s (0h:0m:0s left) Log-likelihood cutoff on original alignment: -1269.385 Iteration 60 / LogL: -1247.772 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 70 / LogL: -1247.793 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 80 / LogL: -1248.058 / Time: 0h:0m:0s (0h:0m:0s left) UPDATE BEST LOG-LIKELIHOOD: -1247.772 Iteration 90 / LogL: -1247.832 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 100 / LogL: -1248.058 / Time: 0h:0m:0s (0h:0m:0s left) Log-likelihood cutoff on original alignment: -1270.376 NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.999 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: -1247.772 Optimal log-likelihood: -1247.772 Rate parameters: A-C: 1.00000 A-G: 2.92011 A-T: 1.00000 C-G: 1.00000 C-T: 2.92011 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.259 Parameters optimization took 1 rounds (0.000 sec) BEST SCORE FOUND : -1247.772 Creating bootstrap support values... Split supports printed to NEXUS file ITS2_small.phy.splits.nex Total tree length: 1.469 Total number of iterations: 102 CPU time used for tree search: 0.542 sec (0h:0m:0s) Wall-clock time used for tree search: 0.554 sec (0h:0m:0s) Total CPU time used: 0.577 sec (0h:0m:0s) Total wall-clock time used: 0.598 sec (0h:0m:0s) Computing bootstrap consensus tree... Reading input file ITS2_small.phy.splits.nex... 8 taxa and 31 splits. Consensus tree written to ITS2_small.phy.contree Reading input trees file ITS2_small.phy.contree Log-likelihood of consensus tree: -1247.772 Analysis results written to: IQ-TREE report: ITS2_small.phy.iqtree Maximum-likelihood tree: ITS2_small.phy.treefile Likelihood distances: ITS2_small.phy.mldist Ultrafast bootstrap approximation results written to: Split support values: ITS2_small.phy.splits.nex Consensus tree: ITS2_small.phy.contree Screen log file: ITS2_small.phy.log Date and Time: Fri Apr 5 13:30:20 2019