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.wireless.yale.internal (AVX2, FMA3, 16 GB RAM) Command: iqtree -s 18s-28s_BLAST-genbankCalanoida_reduced.phy -spp partitions.nex -m MFP -mset mrbayes -bb 1000 Seed: 501734 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Feb 27 17:27:26 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-28s_BLAST-genbankCalanoida_reduced.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences WARNING: 121 sites contain only gaps or ambiguous characters. Alignment has 116 sequences with 3092 columns, 1581 distinct patterns 944 parsimony-informative, 460 singleton sites, 1687 constant sites Gap/Ambiguity Composition p-value 1 Acanthodiaptomus_pacificus 17.30% passed 70.27% 2 Acrocalanus_longicornis 35.90% passed 61.27% 3 Aetideus_armatus 49.32% passed 71.22% 4 Arctodiaptomus_salinus 29.01% passed 89.63% 5 Arctodiaptomus_wierzejskii 29.01% passed 94.22% 6 Bathycalanus_princeps 49.39% passed 98.20% 7 Calanipeda_aquaedulcis 28.85% passed 89.27% 8 Calanoides_carinatus 24.29% passed 98.26% 9 Calanus_finmarchicus 12.58% passed 95.25% 10 Calanus_helgolandicus 22.28% passed 87.31% 11 Calanus_hyperboreus 55.79% passed 47.67% 12 Calanus_pacificus 22.12% passed 86.82% 13 Calanus_propinquus 57.47% passed 29.81% 14 Calanus_sinicus 19.08% passed 74.64% 15 Calocalanus_curtus 35.93% passed 15.54% 16 Calocalanus_minutus 39.33% passed 23.99% 17 Calocalanus_plumulosus 31.73% passed 7.65% 18 Calocalanus_styliremis 36.00% passed 13.76% 19 Candacia_simplex 48.77% passed 68.87% 20 Centropages_abdominalis 23.35% passed 44.98% 21 Centropages_furcatus 18.98% passed 99.76% 22 Centropages_violaceus 49.29% passed 85.98% 23 Clausocalanus_arcuicornis 49.64% passed 37.25% 24 Copidodiaptomus_numidicus 29.01% passed 97.47% 25 Cosmocalanus_darwinii 14.68% passed 87.75% 26 Ctenocalanus_vanus 57.47% passed 21.47% 27 Delibus_nudus 35.87% passed 63.38% 28 Diaixis_hibernica 49.26% passed 92.75% 29 Diaptomus_castor 28.95% passed 96.94% 30 Diaptomus_cyaneus 29.01% passed 96.65% 31 Diaptomus_kenitraensis 29.01% passed 95.68% 32 Diaptomus_mirus 29.01% passed 94.28% 33 Disseta_scopularis 54.20% passed 96.36% 34 Epischura_baikalensis 18.60% passed 47.50% 35 Epischura_chankensis 16.07% passed 48.53% 36 Epischura_fluviatilis 16.04% passed 86.07% 37 Epischura_lacustris 39.46% passed 80.79% 38 Epischura_nevadensis 16.01% passed 77.44% 39 Epischura_nordenskioldi 17.92% passed 96.63% 40 Euchaeta_indica 21.77% passed 85.21% 41 Euchaeta_rimana 22.64% passed 81.15% 42 Eudiaptomus_vulgaris 29.01% passed 96.06% 43 Foxtonia_barbatula 49.26% passed 69.86% 44 Haloptilus_longicornis 21.80% passed 76.16% 45 Heliodiaptomus_kikuchii 19.44% passed 90.94% 46 Hemirhabdus_grimaldii 54.20% passed 94.12% 47 Heterocope_septentrionalis 15.94% passed 74.69% 48 Heterorhabdus_papilliger 54.20% passed 93.18% 49 Heterostylites_longicornis 54.20% passed 91.42% 50 Hyalopontius_typicus 48.32% failed 0.76% 51 Hyperbionyx_athesphatos 49.13% passed 62.12% 52 Limnocalanus_macrurus 20.28% passed 89.08% 53 Lucicutia_flavicornis 49.26% passed 95.86% 54 Mecynocera_clausi 22.74% passed 91.85% 55 Mesorhabdus_brevicaudatus 54.20% passed 97.58% 56 Metridia_effusa 49.35% passed 99.36% 57 Metridia_longa 21.35% passed 99.99% 58 Metridia_lucens 22.12% passed 99.93% 59 Metridia_pacifica 23.06% passed 99.80% 60 Microcalanus_pygmaeus 55.60% passed 13.90% 61 Nannocalanus_minor 65.85% passed 50.12% 62 Neocalanus_cristatus 20.31% passed 98.95% 63 Neocalanus_flemingeri 20.41% passed 99.84% 64 Neocalanus_gracilis 32.66% passed 97.13% 65 Neocalanus_plumchrus 20.38% passed 99.86% 66 Neocalanus_robustior 30.89% passed 95.37% 67 Neodiaptomus_schmackeri 17.01% passed 77.98% 68 Neorhabdus_latus 54.20% passed 94.74% 69 Nullosetigera_auctiseta 49.45% passed 98.71% 70 Paracalanus_aculeatus 32.83% passed 98.14% 71 Paracalanus_indicus 28.14% passed 86.27% 72 Paracalanus_denudatus 27.43% passed 83.50% 73 Paracalanus_parvus 14.20% passed 94.61% 74 Paracalanus_tropicus 28.10% passed 58.40% 75 Paraeuchaeta_glacialis 55.85% passed 27.31% 76 Paraeuchaeta_norvegica 54.01% passed 41.89% 77 Paraheterorhabdus_compactus 49.29% passed 97.32% 78 Paraugaptilus_buchani 49.09% passed 82.00% 79 Pareucalanus_attenuatus 30.92% passed 68.64% 80 Phaenna_spinifera 48.22% passed 70.73% 81 Pinkertonius_ambiguus 56.02% failed 1.32% 82 Pleuromamma_abdominalis 21.86% passed 99.57% 83 Pleuromamma_xiphias 22.22% passed 98.46% 84 Pontellina_plumata 22.54% passed 38.07% 85 Pseudocyclops_juanibali 22.06% passed 5.58% 86 Pseudocyclops_schminkei 24.42% passed 16.23% 87 Pseudodiaptomus_inopinus 11.87% passed 16.96% 88 Pseudodiaptomus_marinus 16.62% passed 64.69% 89 Pseudodiaptomus_nihonkaiensis 16.98% passed 97.44% 90 Rhincalanus_cornutus 24.68% passed 51.68% 91 Rhincalanus_nasutus 21.83% passed 76.62% 92 Rhincalanus_rostrifrons 27.88% passed 54.76% 93 Scolecithrix_bradyi 49.35% passed 85.45% 94 Scolecithrix_danae 22.90% passed 99.44% 95 Sinocalanus_tenellus 15.91% passed 89.29% 96 Sinodiaptomus_sarsi 17.08% passed 91.24% 97 Spinocalanus_abyssalis 49.29% passed 42.40% 98 Spinocalanus_angusticeps 23.84% passed 88.85% 99 Spinocalanus_elongatus 22.99% passed 51.03% 100 Spinocalanus_horridus 22.90% passed 54.06% 101 Spinocalanus_spinosus 23.80% passed 84.85% 102 Subeucalanus_crassus 30.89% passed 49.52% 103 Subeucalanus_pileatus_2 21.99% passed 77.60% 104 Subeucalanus_pileatus_1 35.35% passed 34.62% 105 Subeucalanus_subcrassus 32.21% passed 50.39% 106 Subeucalanus_subtenuis 21.73% passed 84.72% 107 Sulcanus_conflictus 49.35% passed 58.85% 108 Temora_discaudata 15.59% passed 97.05% 109 Temora_longicornis 20.80% passed 42.35% 110 Temora_turbinata 16.36% passed 78.72% 111 Temorites_brevis 49.35% passed 98.01% 112 Temoropia_mayumbaensis 49.26% passed 94.15% 113 Tharybis_groenlandica 49.29% passed 98.47% 114 Tigriopus_japonicus 15.14% passed 13.45% 115 Tortanus_gracilis 48.87% passed 52.58% 116 Undeuchaeta_major 23.06% passed 94.84% WARNING: 14 sequences contain more than 50% gaps/ambiguity **** TOTAL 32.49% 2 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: No CharPartition defined, use all CharSets Loading 2 partitions... Subset Type Seqs Sites Infor Invar Model Name 1 116 1928 468 1211 MFP 18s 2 116 1164 476 477 MFP 28s Degree of missing data: 0.000 Info: multi-threading strategy over partitions Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.030 seconds NOTE: ModelFinder requires 66 MB RAM! Testing GTR+F+G on supermatrix... GTR+F+G4 / LnL: -34581.893 / df: 238 / AIC: 69639.787 / AICc: 69679.662 / BIC: 71076.491 Selecting individual models for 2 charsets using BIC... No. Model Score Charset 1 GTR+F+R4 32623.092 18s 2 GTR+F+R4 35997.339 28s Full partition model BIC score: 70474.509 (LnL: -34200.537 df:258) 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: 93.944 seconds (0h:1m:33s) Wall-clock time for ModelFinder: 95.804 seconds (0h:1m:35s) Generating 1000 samples for ultrafast bootstrap (seed: 501734)... NOTE: 30 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -36433.074 Current log-likelihood at step 1: -34407.258 Current log-likelihood at step 2: -34331.261 Current log-likelihood at step 3: -34297.799 Current log-likelihood at step 4: -34275.649 Current log-likelihood at step 5: -34260.391 Current log-likelihood at step 6: -34249.608 Current log-likelihood at step 7: -34241.841 Current log-likelihood at step 8: -34236.080 Current log-likelihood at step 9: -34231.584 Current log-likelihood at step 10: -34227.949 Current log-likelihood at step 11: -34224.966 Current log-likelihood at step 12: -34222.456 Current log-likelihood at step 13: -34220.320 Current log-likelihood at step 14: -34218.496 Current log-likelihood at step 15: -34216.945 Current log-likelihood at step 16: -34215.683 Current log-likelihood at step 17: -34214.565 Current log-likelihood at step 18: -34213.556 Current log-likelihood at step 19: -34212.636 Current log-likelihood at step 20: -34211.816 Current log-likelihood at step 21: -34211.065 Current log-likelihood at step 22: -34210.380 Current log-likelihood at step 23: -34209.756 Current log-likelihood at step 24: -34209.179 Current log-likelihood at step 25: -34208.681 Current log-likelihood at step 26: -34208.244 Current log-likelihood at step 27: -34207.808 Current log-likelihood at step 28: -34207.449 Current log-likelihood at step 29: -34207.097 Current log-likelihood at step 30: -34206.764 Current log-likelihood at step 31: -34206.444 Current log-likelihood at step 32: -34206.132 Current log-likelihood at step 33: -34205.825 Current log-likelihood at step 34: -34205.523 Current log-likelihood at step 35: -34205.221 Current log-likelihood at step 36: -34204.918 Current log-likelihood at step 37: -34204.610 Current log-likelihood at step 38: -34204.295 Current log-likelihood at step 39: -34203.968 Current log-likelihood at step 40: -34203.624 Current log-likelihood at step 41: -34203.259 Current log-likelihood at step 42: -34202.871 Current log-likelihood at step 43: -34202.452 Current log-likelihood at step 44: -34201.995 Current log-likelihood at step 45: -34201.500 Current log-likelihood at step 46: -34200.964 Current log-likelihood at step 47: -34200.391 Current log-likelihood at step 48: -34199.793 Current log-likelihood at step 49: -34199.183 Current log-likelihood at step 50: -34198.586 Current log-likelihood at step 51: -34198.018 Current log-likelihood at step 52: -34197.499 Current log-likelihood at step 53: -34197.034 Current log-likelihood at step 54: -34196.629 Current log-likelihood at step 55: -34196.277 Current log-likelihood at step 56: -34195.976 Current log-likelihood at step 57: -34195.722 Current log-likelihood at step 58: -34195.497 Current log-likelihood at step 59: -34195.300 Current log-likelihood at step 60: -34195.126 Current log-likelihood at step 61: -34194.972 Current log-likelihood at step 62: -34194.832 Current log-likelihood at step 63: -34194.705 Current log-likelihood at step 64: -34194.587 Current log-likelihood at step 65: -34194.477 Current log-likelihood at step 66: -34194.373 Current log-likelihood at step 67: -34194.275 Partition-specific rates: 0.535 1.769 Parameters optimization took 66 rounds (35.651 sec) Computing ML distances based on estimated model parameters... 0.261 sec Computing BIONJ tree... 0.008 seconds Log-likelihood of BIONJ tree: -34254.490 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 2.583 second Computing log-likelihood of 98 initial trees ... 7.684 seconds Current best score: -34156.419 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -34125.264 Current log-likelihood at step 1: -34124.877 Current log-likelihood at step 2: -34124.786 Parameters optimization took 1 rounds (1.009 sec) BETTER TREE FOUND at iteration 1: -34124.786 Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -34121.802 Current log-likelihood at step 1: -34121.630 Current log-likelihood at step 2: -34121.573 Parameters optimization took 1 rounds (0.834 sec) BETTER TREE FOUND at iteration 2: -34121.573 Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -34114.552 Current log-likelihood at step 1: -34114.366 Current log-likelihood at step 2: -34114.321 Parameters optimization took 1 rounds (0.922 sec) BETTER TREE FOUND at iteration 4: -34114.321 Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -34098.088 Current log-likelihood at step 1: -34097.360 Current log-likelihood at step 2: -34097.276 Parameters optimization took 1 rounds (1.097 sec) BETTER TREE FOUND at iteration 6: -34097.276 Iteration 10 / LogL: -34135.179 / Time: 0h:0m:58s Iteration 20 / LogL: -34112.522 / Time: 0h:1m:6s Finish initializing candidate tree set (18) Current best tree score: -34097.276 / CPU time: 30.481 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -34093.986 Current log-likelihood at step 1: -34093.750 Current log-likelihood at step 2: -34093.679 Parameters optimization took 1 rounds (1.008 sec) BETTER TREE FOUND at iteration 21: -34093.679 Iteration 30 / LogL: -34097.193 / Time: 0h:1m:17s (0h:4m:3s left) UPDATE BEST LOG-LIKELIHOOD: -34093.677 Iteration 40 / LogL: -34107.846 / Time: 0h:1m:26s (0h:2m:59s left) Estimate model parameters (epsilon = 0.100) Initial log-likelihood: -34092.000 Current log-likelihood at step 1: -34091.856 Current log-likelihood at step 2: -34091.816 Parameters optimization took 1 rounds (0.965 sec) BETTER TREE FOUND at iteration 43: -34091.816 Iteration 50 / LogL: -34152.621 / Time: 0h:1m:36s (0h:3m:3s left) Log-likelihood cutoff on original alignment: -34162.838 Iteration 60 / LogL: -34093.695 / Time: 0h:1m:46s (0h:2m:29s left) Iteration 70 / LogL: -34092.464 / Time: 0h:1m:54s (0h:2m:1s left) Iteration 80 / LogL: -34097.816 / Time: 0h:2m:4s (0h:1m:39s left) Iteration 90 / LogL: -34092.323 / Time: 0h:2m:13s (0h:1m:19s left) UPDATE BEST LOG-LIKELIHOOD: -34091.811 Iteration 100 / LogL: -34091.811 / Time: 0h:2m:23s (0h:1m:2s left) Log-likelihood cutoff on original alignment: -34162.838 NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998 UPDATE BEST LOG-LIKELIHOOD: -34091.809 UPDATE BEST LOG-LIKELIHOOD: -34091.809 Iteration 110 / LogL: -34091.809 / Time: 0h:2m:33s (0h:2m:6s left) Iteration 120 / LogL: -34111.380 / Time: 0h:2m:42s (0h:1m:49s left) Iteration 130 / LogL: -34092.549 / Time: 0h:2m:51s (0h:1m:33s left) Iteration 140 / LogL: -34114.759 / Time: 0h:3m:1s (0h:1m:18s left) UPDATE BEST LOG-LIKELIHOOD: -34091.808 TREE SEARCH COMPLETED AFTER 144 ITERATIONS / Time: 0h:3m:4s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) Initial log-likelihood: -34091.808 Current log-likelihood at step 1: -34091.756 Current log-likelihood at step 2: -34091.721 Current log-likelihood at step 3: -34091.689 Current log-likelihood at step 4: -34091.665 Current log-likelihood at step 5: -34091.640 Current log-likelihood at step 6: -34091.618 Current log-likelihood at step 7: -34091.596 Current log-likelihood at step 8: -34091.575 Current log-likelihood at step 9: -34091.557 Current log-likelihood at step 10: -34091.538 Current log-likelihood at step 11: -34091.524 Current log-likelihood at step 12: -34091.511 Current log-likelihood at step 13: -34091.496 Current log-likelihood at step 14: -34091.482 Current log-likelihood at step 15: -34091.470 Current log-likelihood at step 16: -34091.458 Current log-likelihood at step 17: -34091.445 Current log-likelihood at step 18: -34091.436 Partition-specific rates: 0.525 1.786 Parameters optimization took 17 rounds (7.397 sec) BEST SCORE FOUND : -34091.436 Creating bootstrap support values... Split supports printed to NEXUS file partitions.nex.splits.nex Total tree length: 4.038 Total number of iterations: 144 CPU time used for tree search: 147.733 sec (0h:2m:27s) Wall-clock time used for tree search: 148.412 sec (0h:2m:28s) Total CPU time used: 191.523 sec (0h:3m:11s) Total wall-clock time used: 192.603 sec (0h:3m:12s) Computing bootstrap consensus tree... Reading input file partitions.nex.splits.nex... 116 taxa and 467 splits. Consensus tree written to partitions.nex.contree Reading input trees file partitions.nex.contree Log-likelihood of consensus tree: -34092.082 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: Wed Feb 27 17:32:15 2019