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-ITS2-28s_small.phy -spp partitions.nex -m MFP -mset mrbayes -bb 1000 -o Pontellina_plumata Seed: 980826 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Apr 5 13:41:00 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 partition model file partitions.nex ... Reading alignment file 18s-ITS2-28s_small.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 9 sequences with 2924 columns, 377 distinct patterns 185 parsimony-informative, 300 singleton sites, 2439 constant sites Gap/Ambiguity Composition p-value 1 Pontellina_plumata 10.53% passed 84.77% 2 Temora_discaudata 2.63% passed 64.71% 3 Epischura_baikalensis 5.71% passed 74.28% 4 Epischura_chankensis 3.69% passed 88.36% 5 Heterocope_septentrionalis 3.04% passed 98.64% 6 Epischura_fluviatilis 2.94% passed 99.05% 7 Epischura_nevadensis 2.60% passed 93.75% 8 Epischura_nordenskioldi 13.20% passed 97.22% 9 Epischura_lacustris 27.36% passed 88.14% **** TOTAL 7.97% 0 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: No CharPartition defined, use all CharSets Loading 3 partitions... Subset Type Seqs Sites Infor Invar Model Name 1 9 1710 56 1547 MFP 18s 2 8 267 70 116 MFP ITS2 3 9 947 59 776 MFP 28s Degree of missing data: 0.010 Info: multi-threading strategy over partitions Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds NOTE: ModelFinder requires 2 MB RAM! Testing GTR+F+G on supermatrix... GTR+F+G4 / LnL: -7409.179 / df: 24 / AIC: 14866.358 / AICc: 14866.771 / BIC: 15009.895 Selecting individual models for 3 charsets using BIC... No. Model Score Charset 1 HKY+F+I 6983.337 18s 2 K2P+I 2536.883 ITS2 3 SYM+R2 5034.064 28s Full partition model BIC score: 14685.433 (LnL: -7219.016 df:31) Partition information was printed to partitions.nex.best_scheme.nex Partition information in Raxml format was printed to partitions.nex.best_scheme All model information printed to partitions.nex.model.gz CPU time for ModelFinder: 0.478 seconds (0h:0m:0s) Wall-clock time for ModelFinder: 0.495 seconds (0h:0m:0s) Generating 1000 samples for ultrafast bootstrap (seed: 980826)... NOTE: 1 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -7599.905 Current log-likelihood at step 1: -7272.857 Current log-likelihood at step 2: -7247.610 Current log-likelihood at step 3: -7232.409 Current log-likelihood at step 4: -7230.157 Current log-likelihood at step 5: -7228.608 Current log-likelihood at step 6: -7227.587 Current log-likelihood at step 7: -7226.963 Current log-likelihood at step 8: -7226.599 Current log-likelihood at step 9: -7226.380 Current log-likelihood at step 10: -7226.232 Current log-likelihood at step 11: -7226.112 Current log-likelihood at step 12: -7225.996 Current log-likelihood at step 13: -7225.872 Current log-likelihood at step 14: -7225.737 Current log-likelihood at step 15: -7225.588 Current log-likelihood at step 16: -7225.425 Current log-likelihood at step 17: -7225.246 Current log-likelihood at step 18: -7225.049 Current log-likelihood at step 19: -7224.837 Current log-likelihood at step 20: -7224.611 Current log-likelihood at step 21: -7224.369 Current log-likelihood at step 22: -7224.110 Current log-likelihood at step 23: -7223.837 Current log-likelihood at step 24: -7223.549 Current log-likelihood at step 25: -7223.247 Current log-likelihood at step 26: -7222.932 Current log-likelihood at step 27: -7222.604 Current log-likelihood at step 28: -7222.268 Current log-likelihood at step 29: -7221.922 Current log-likelihood at step 30: -7221.565 Current log-likelihood at step 31: -7221.210 Current log-likelihood at step 32: -7220.852 Current log-likelihood at step 33: -7220.502 Current log-likelihood at step 34: -7220.166 Current log-likelihood at step 35: -7219.846 Current log-likelihood at step 36: -7219.552 Current log-likelihood at step 37: -7219.286 Current log-likelihood at step 38: -7219.052 Current log-likelihood at step 39: -7218.849 Current log-likelihood at step 40: -7218.680 Current log-likelihood at step 41: -7218.539 Current log-likelihood at step 42: -7218.427 Current log-likelihood at step 43: -7218.341 Partition-specific rates: 0.373 4.324 1.195 Parameters optimization took 42 rounds (0.124 sec) Computing ML distances based on estimated model parameters... 0.001 sec Computing BIONJ tree... 0.000 seconds Log-likelihood of BIONJ tree: -7283.487 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.085 second Computing log-likelihood of 80 initial trees ... 0.087 seconds Current best score: -7218.341 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -7218.341 Current log-likelihood at step 1: -7218.273 Parameters optimization took 0 rounds (0.002 sec) BETTER TREE FOUND at iteration 1: -7218.273 Iteration 10 / LogL: -7218.278 / Time: 0h:0m:0s Iteration 20 / LogL: -7218.279 / Time: 0h:0m:0s Finish initializing candidate tree set (1) Current best tree score: -7218.273 / CPU time: 0.321 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- UPDATE BEST LOG-LIKELIHOOD: -7218.273 Iteration 30 / LogL: -7218.275 / Time: 0h:0m:0s (0h:0m:1s left) Iteration 40 / LogL: -7218.273 / Time: 0h:0m:0s (0h:0m:1s left) Iteration 50 / LogL: -7218.275 / Time: 0h:0m:0s (0h:0m:0s left) Log-likelihood cutoff on original alignment: -7244.436 Iteration 60 / LogL: -7218.278 / Time: 0h:0m:0s (0h:0m:0s left) Iteration 70 / LogL: -7218.285 / Time: 0h:0m:1s (0h:0m:0s left) Iteration 80 / LogL: -7218.285 / Time: 0h:0m:1s (0h:0m:0s left) Iteration 90 / LogL: -7218.285 / Time: 0h:0m:1s (0h:0m:0s left) Iteration 100 / LogL: -7218.333 / Time: 0h:0m:1s (0h:0m:0s left) Log-likelihood cutoff on original alignment: -7244.436 NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000 TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:1s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) Initial log-likelihood: -7218.273 Current log-likelihood at step 1: -7218.223 Current log-likelihood at step 2: -7218.187 Current log-likelihood at step 3: -7218.160 Current log-likelihood at step 4: -7218.140 Current log-likelihood at step 5: -7218.126 Current log-likelihood at step 6: -7218.116 Current log-likelihood at step 7: -7218.109 Partition-specific rates: 0.373 4.328 1.193 Parameters optimization took 6 rounds (0.016 sec) BEST SCORE FOUND : -7218.109 Creating bootstrap support values... Split supports printed to NEXUS file partitions.nex.splits.nex Total tree length: 0.343 Total number of iterations: 102 CPU time used for tree search: 1.230 sec (0h:0m:1s) Wall-clock time used for tree search: 1.245 sec (0h:0m:1s) Total CPU time used: 1.427 sec (0h:0m:1s) Total wall-clock time used: 1.460 sec (0h:0m:1s) Computing bootstrap consensus tree... Reading input file partitions.nex.splits.nex... 9 taxa and 27 splits. Consensus tree written to partitions.nex.contree Reading input trees file partitions.nex.contree Log-likelihood of consensus tree: -7218.109 Analysis results written to: IQ-TREE report: partitions.nex.iqtree Maximum-likelihood tree: partitions.nex.treefile Likelihood distances: partitions.nex.mldist Best partitioning scheme: partitions.nex.best_scheme.nex in RAxML format: partitions.nex.best_scheme Ultrafast bootstrap approximation results written to: Split support values: partitions.nex.splits.nex Consensus tree: partitions.nex.contree Screen log file: partitions.nex.log Date and Time: Fri Apr 5 13:41:02 2019