oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo --- PhyML 3.3.20190909 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Sequence filename: big2_1_phy . Data set: #1 . Initial tree: BioNJ . Model of amino acids substitution: WAG . Number of taxa: 438 . Log-likelihood: -98162.65847 . Unconstrained log-likelihood: -1225.04091 . Composite log-likelihood: -292320.44038 . Parsimony: 20238 . Tree size: 108.24501 . Discrete gamma model: Yes - Number of classes: 4 - Gamma shape parameter: 1.338 - Relative rate in class 1: 0.19918 [freq=0.250000] - Relative rate in class 2: 0.55917 [freq=0.250000] - Relative rate in class 3: 1.03930 [freq=0.250000] - Relative rate in class 4: 2.20236 [freq=0.250000] . Proportion of invariant: 0.004 . Run ID: none . Random seed: 1632878998 . Subtree patterns aliasing: no . Version: 3.3.20190909 . Time used: 1h40m26s (6026 seconds) oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Suggested citations: S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0." Systematic Biology. 2010. 59(3):307-321. S. Guindon & O. Gascuel "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood" Systematic Biology. 2003. 52(5):696-704. oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Starting SMS v1.8.4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Input alignment : big2_1_phy Data type : Protein Number of taxa : 438 Number of sites : 226 Number of branches : 873 Criterion : AIC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Step 1 : Set a fixed topology ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Step 2 : Select the best decoration AIC=200316.55746 decoration : '+G+I' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Step 3 : Select the best matrix AIC=199791.27018 matrix : 'WAG' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Step 4 : Select the best final decoration AIC=199440.11740 decoration : '+G+I' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Selected model : WAG +G+I ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Substitution model : WAG Equilibrium frequencies : Model Proportion of invariable sites : estimated (0.004) Number of substitution rate categories : 4 Gamma shape parameter : estimated (1.338) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Suggested citations: SMS Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel. "SMS: Smart Model Selection in PhyML." Molecular Biology and Evolution, msx149, 2017. PhyML S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel "New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0." Systematic Biology. 2010. 59(3):307-321. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Additional step : Infer tree with model : 'WAG +G+I' . The NNI option is deprecated. PhyML now uses a mix of SPRs and NNIs. . Command line: /data/http/www/binaries/phyml/../sms/sms/phyml-src/phyml -i /data/http/www/exec/20210929-031943_Oh83/big2_1_phy -d aa -o tlr -m WAG -c 4 -a 1.338 -v 0.004 -f m -s NNI -b -5 --leave_duplicates --no_memory_check --print_trace --json_trace ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// . Sequence filename: big2_1_phy . Data type: aa . Alphabet size: 20 . Sequence format: interleaved . Number of data sets: 1 . Nb of bootstrapped data sets: 0 . Compute approximate likelihood ratio test: yes (aBayes branch supports) . Model name: WAG . Proportion of invariable sites: 0.004000 . Number of subst. rate catgs: 4 . Gamma distribution parameter: 1.338000 . 'Middle' of each rate class: mean . Amino acid equilibrium frequencies: model . Optimise tree topology: yes . Starting tree: BioNJ . Add random input tree: no . Optimise branch lengths: yes . Minimum length of an edge: 1e-08 . Optimise substitution model parameters: no . Run ID: none . Random seed: 1632878998 . Subtree patterns aliasing: no . Version: 3.3.20190909 . Byte alignment: 32 . AVX enabled: yes . SSE enabled: yes ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// . 226 patterns found (out of a total of 226 sites). . 1 sites without polymorphism (0.44%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 267 MB of memory space. . Score of initial tree: -99820.78 . Starting first round of SPRs... 562s | 1 | lnL= -98772.5 | depth= 9/ 110 | improvements= 312 | delta_lnL= 228.8/ 1000.0 + 1095s | 2 | lnL= -98799.3 | depth= 11/ 66 | improvements= 311 | delta_lnL= 301.7/ 1000.0 1620s | 3 | lnL= -98679.2 | depth= 7/ 39 | improvements= 329 | delta_lnL= 115.2/ 1000.0 + 2069s | 4 | lnL= -98649.0 | depth= 7/ 23 | improvements= 267 | delta_lnL= 183.5/ 1000.0 + 2268s | 5 | lnL= -98597.4 | depth= 6/ 13 | improvements= 267 | delta_lnL= 88.1/ 1000.0 + 2452s | 6 | lnL= -98696.3 | depth= 11/ 12 | improvements= 275 | delta_lnL= 45.6/ 603.4 2731s | 7 | lnL= -98616.2 | depth= 10/ 17 | improvements= 257 | delta_lnL= 57.0/ 603.4 2997s | 8 | lnL= -98548.7 | depth= 6/ 16 | improvements= 240 | delta_lnL= 29.2/ 603.4 + 3179s | 9 | lnL= -98505.7 | depth= 7/ 12 | improvements= 240 | delta_lnL= 82.5/ 603.4 + 3259s | 10 | lnL= -98478.5 | depth= 7/ 13 | improvements= 211 | delta_lnL= 89.2/ 113.9 + 3340s | 11 | lnL= -98368.3 | depth= 9/ 13 | improvements= 181 | delta_lnL= 70.3/ 113.9 + 3419s | 12 | lnL= -98368.6 | depth= 7/ 15 | improvements= 180 | delta_lnL= 27.3/ 113.9 3499s | 13 | lnL= -98404.0 | depth= 6/ 13 | improvements= 164 | delta_lnL= 30.7/ 113.9 3593s | 14 | lnL= -98428.3 | depth= 6/ 12 | improvements= 135 | delta_lnL= 51.8/ 178.4 3681s | 15 | lnL= -98294.4 | depth= 4/ 12 | improvements= 106 | delta_lnL= 15.4/ 178.4 + 3760s | 16 | lnL= -98278.0 | depth= 8/ 10 | improvements= 103 | delta_lnL= 49.5/ 178.4 + 3856s | 17 | lnL= -98244.9 | depth= 11/ 14 | improvements= 60 | delta_lnL= 11.9/ 178.4 + 3915s | 18 | lnL= -98232.7 | depth= 7/ 17 | improvements= 48 | delta_lnL= 9.7/ 103.7 + 3976s | 19 | lnL= -98234.4 | depth= 5/ 13 | improvements= 51 | delta_lnL= 9.7/ 103.7 4028s | 20 | lnL= -98227.9 | depth= 4/ 11 | improvements= 39 | delta_lnL= 15.3/ 103.7 + 4080s | 21 | lnL= -98217.0 | depth= 4/ 10 | improvements= 52 | delta_lnL= 12.8/ 103.7 + 4110s | 22 | lnL= -98233.9 | depth= 7/ 10 | improvements= 44 | delta_lnL= 25.1/ 50.0 4140s | 23 | lnL= -98219.6 | depth= 6/ 13 | improvements= 44 | delta_lnL= 10.1/ 50.0 4167s | 24 | lnL= -98243.4 | depth= 7/ 12 | improvements= 27 | delta_lnL= 21.9/ 50.0 4197s | 25 | lnL= -98222.3 | depth= 3/ 13 | improvements= 40 | delta_lnL= 18.9/ 50.0 4223s | 26 | lnL= -98214.4 | depth= 4/ 9 | improvements= 24 | delta_lnL= 7.6/ 50.1 + 4251s | 27 | lnL= -98215.7 | depth= 6/ 10 | improvements= 33 | delta_lnL= 21.8/ 50.1 4279s | 28 | lnL= -98227.3 | depth= 9/ 12 | improvements= 32 | delta_lnL= 8.5/ 50.1 4309s | 29 | lnL= -98221.7 | depth= 3/ 15 | improvements= 42 | delta_lnL= 5.0/ 50.1 4336s | 30 | lnL= -98207.0 | depth= 8/ 9 | improvements= 31 | delta_lnL= 23.4/ 50.0 + 4367s | 31 | lnL= -98200.3 | depth= 7/ 14 | improvements= 22 | delta_lnL= 31.4/ 50.0 + 4393s | 32 | lnL= -98215.2 | depth= 5/ 13 | improvements= 23 | delta_lnL= 8.3/ 50.0 4421s | 33 | lnL= -98212.8 | depth= 3/ 11 | improvements= 25 | delta_lnL= 5.5/ 50.0 4457s | 34 | lnL= -98206.0 | depth= 3/ 9 | improvements= 22 | delta_lnL= 14.9/ 62.8 4488s | 35 | lnL= -98204.4 | depth= 7/ 9 | improvements= 22 | delta_lnL= 22.8/ 62.8 4519s | 36 | lnL= -98221.7 | depth= 4/ 13 | improvements= 23 | delta_lnL= 9.0/ 62.8 4548s | 37 | lnL= -98208.5 | depth= 3/ 10 | improvements= 14 | delta_lnL= 13.4/ 62.8 . Second round of optimization... 4576s | 38 | lnL= -98203.0 | depth= 3/ 13 | improvements= 33 | delta_lnL= 12.9/ 50.0 4603s | 39 | lnL= -98204.2 | depth= 3/ 10 | improvements= 32 | delta_lnL= 7.0/ 50.0 4631s | 40 | lnL= -98191.2 | depth= 2/ 8 | improvements= 34 | delta_lnL= 4.3/ 50.0 + 4665s | 41 | lnL= -98192.1 | depth= 2/ 6 | improvements= 33 | delta_lnL= 3.1/ 50.0 4683s | 42 | lnL= -98195.6 | depth= 2/ 6 | improvements= 27 | delta_lnL= 11.2/ 25.7 4701s | 43 | lnL= -98191.3 | depth= 3/ 6 | improvements= 23 | delta_lnL= 8.0/ 25.7 4718s | 44 | lnL= -98184.5 | depth= 7/ 7 | improvements= 21 | delta_lnL= 20.6/ 25.7 + 4738s | 45 | lnL= -98196.4 | depth= 3/ 11 | improvements= 32 | delta_lnL= 4.7/ 25.7 4760s | 46 | lnL= -98201.8 | depth= 1/ 8 | improvements= 24 | delta_lnL= 0.0/ 41.2 4782s | 47 | lnL= -98197.2 | depth= 3/ 6 | improvements= 29 | delta_lnL= 2.3/ 41.2 4804s | 48 | lnL= -98190.2 | depth= 2/ 7 | improvements= 23 | delta_lnL= 7.5/ 41.2 4824s | 49 | lnL= -98187.2 | depth= 1/ 6 | improvements= 19 | delta_lnL= 0.0/ 41.2 4841s | 50 | lnL= -98187.1 | depth= 2/ 5 | improvements= 25 | delta_lnL= 3.2/ 20.0 4863s | 51 | lnL= -98184.6 | depth= 2/ 6 | improvements= 19 | delta_lnL= 5.2/ 20.0 4878s | 52 | lnL= -98193.4 | depth= 2/ 6 | improvements= 22 | delta_lnL= 3.3/ 20.0 4896s | 53 | lnL= -98179.3 | depth= 2/ 6 | improvements= 33 | delta_lnL= 2.4/ 20.0 + 4912s | 54 | lnL= -98185.6 | depth= 1/ 6 | improvements= 19 | delta_lnL= 0.0/ 20.0 4927s | 55 | lnL= -98185.2 | depth= 2/ 5 | improvements= 22 | delta_lnL= 0.2/ 20.0 4943s | 56 | lnL= -98180.3 | depth= 2/ 6 | improvements= 17 | delta_lnL= 5.9/ 20.0 4958s | 57 | lnL= -98176.7 | depth= 3/ 6 | improvements= 14 | delta_lnL= 2.3/ 20.0 + 4973s | 58 | lnL= -98179.8 | depth= 2/ 7 | improvements= 16 | delta_lnL= 2.3/ 20.0 4990s | 59 | lnL= -98183.9 | depth= 3/ 6 | improvements= 17 | delta_lnL= 12.1/ 20.0 5005s | 60 | lnL= -98181.3 | depth= 1/ 7 | improvements= 17 | delta_lnL= 0.0/ 20.0 5027s | 61 | lnL= -98186.0 | depth= 5/ 5 | improvements= 22 | delta_lnL= 5.3/ 20.0 5042s | 62 | lnL= -98184.1 | depth= 3/ 9 | improvements= 12 | delta_lnL= 3.1/ 24.2 5060s | 63 | lnL= -98179.7 | depth= 2/ 7 | improvements= 14 | delta_lnL= 4.7/ 24.2 5076s | 64 | lnL= -98183.1 | depth= 2/ 6 | improvements= 16 | delta_lnL= 0.7/ 24.2 5092s | 65 | lnL= -98186.0 | depth= 2/ 6 | improvements= 16 | delta_lnL= 0.7/ 24.2 5106s | 66 | lnL= -98174.6 | depth= 3/ 6 | improvements= 14 | delta_lnL= 3.5/ 20.0 + 5120s | 67 | lnL= -98171.9 | depth= 1/ 7 | improvements= 10 | delta_lnL= 0.0/ 20.0 + 5133s | 68 | lnL= -98173.2 | depth= 1/ 5 | improvements= 8 | delta_lnL= 0.0/ 20.0 5147s | 69 | lnL= -98173.0 | depth= 2/ 5 | improvements= 9 | delta_lnL= 4.9/ 20.0 5161s | 70 | lnL= -98174.8 | depth= 1/ 6 | improvements= 11 | delta_lnL= 0.0/ 20.0 5181s | 71 | lnL= -98166.0 | depth= 2/ 5 | improvements= 10 | delta_lnL= 1.8/ 20.0 + 5195s | 72 | lnL= -98171.5 | depth= 1/ 6 | improvements= 15 | delta_lnL= 0.0/ 20.0 5208s | 73 | lnL= -98171.3 | depth= 1/ 5 | improvements= 6 | delta_lnL= 0.0/ 20.0 5223s | 74 | lnL= -98173.2 | depth= 1/ 5 | improvements= 7 | delta_lnL= 0.0/ 20.0 5236s | 75 | lnL= -98170.1 | depth= 1/ 5 | improvements= 5 | delta_lnL= 0.0/ 20.0 . Third round of optimization... 5422s | 76 | lnL= -98163.0 | depth= 1/ 10 | improvements= 6 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 5611s | 77 | lnL= -98162.8 | depth= 0/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 5807s | 78 | lnL= -98162.7 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 6002s | 79 | lnL= -98162.7 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + . Final optimisation steps... . Log likelihood of the current tree: -98162.658465761167462915182. . Calculating fast branch supports (using 'aBayes'). . Printing the most likely tree in file 'big2_1_phy_phyml_tree.txt'. . Time used 1h40m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo