.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2932_68x1712_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 1264 patterns found. (out of a total of 1712 sites) . 601 sites without polymorphism (35.11%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 45Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 8 sec) [ -15465.7212] [GTR parameters ] . ( 8 sec) [ -15431.9484] [Alpha ][ 0.613860] . ( 9 sec) [ -15431.3316] [ 3250] [depth= 1] . ( 11 sec) [ -15416.2698] [ 3267] [depth= 1] . ( 12 sec) [ -15373.0330] [ 3267] [depth= 1] . ( 13 sec) [ -15369.9974] [ 3268] [depth= 1] . ( 14 sec) [ -15364.6853] [ 3268] [depth= 1] . ( 14 sec) [ -15355.8787] [ 3268] [depth= 1] . ( 14 sec) [ -15354.5441] [ 3268] [depth= 1] . ( 14 sec) [ -15352.9386] [ 3268] [depth= 1] . ( 15 sec) [ -15284.2816] [ 3257] [depth= 2] . ( 15 sec) [ -15281.0539] [ 3257] [depth= 1] . ( 16 sec) [ -15266.4570] [ 3236] [depth= 1] . ( 16 sec) [ -15256.6505] [ 3227] [depth= 1] . ( 17 sec) [ -15254.2275] [ 3223] [depth= 1] . ( 17 sec) [ -15246.2091] [ 3222] [depth= 1] . ( 17 sec) [ -15219.4525] [ 3219] [depth= 1] . ( 18 sec) [ -15218.7551] [ 3219] [depth= 1] . ( 18 sec) [ -15217.8194] [ 3219] [depth= 1] . ( 18 sec) [ -15217.8041] [ 3219] [depth= 5] . ( 18 sec) [ -15215.6028] [ 3219] [depth= 7] . ( 19 sec) [ -15210.9706] [ 3218] [depth= 5] . ( 19 sec) [ -15209.4895] [ 3218] [depth= 3] . ( 20 sec) [ -15199.6480] [ 3218] [depth= 1] . ( 20 sec) [ -15192.4778] [ 3217] [depth= 1] . ( 20 sec) [ -15190.4227] [ 3218] [depth= 3] . ( 20 sec) [ -15190.0678] [ 3218] [depth= 2] . ( 21 sec) [ -15186.6534] [ 3218] [depth= 2] . ( 21 sec) [ -15186.5805] [ 3218] [depth= 1] . ( 22 sec) [ -15180.0194] [ 3217] [depth= 1] . ( 22 sec) [ -15179.6859] [ 3217] [depth= 4] . ( 23 sec) [ -15178.7041] [ 3218] [depth= 2] . ( 23 sec) [ -15175.9009] [ 3221] [depth= 1] . ( 23 sec) [ -15153.2916] [ 3225] [depth= 1] . ( 24 sec) [ -15149.0914] [ 3236] [depth= 1] . ( 25 sec) [ -15147.9753] [ 3236] [depth= 1] . ( 26 sec) [ -15146.0631] [ 3236] [depth= 1] . ( 27 sec) [ -15137.3456] [ 3252] [depth= 2] . ( 27 sec) [ -15135.1717] [ 3248] [depth= 2] . ( 27 sec) [ -15132.6614] [ 3230] [depth= 3] . ( 27 sec) [ -15130.6820] [ 3230] [depth= 1] . ( 27 sec) [ -15128.7066] [ 3230] [depth= 1] . ( 29 sec) [ -15126.9949] [ 3230] [depth= 1] . ( 29 sec) [ -15126.8894] [ 3230] [depth= 1] . ( 30 sec) [ -15126.1262] [ 3229] [depth= 2] . ( 31 sec) [ -15120.8865] [ 3228] [depth= 4] . ( 31 sec) [ -15120.8132] [ 3228] [depth= 2] . ( 31 sec) [ -15120.7992] [ 3228] [depth= 3] . ( 32 sec) [ -15120.5594] [ 3228] [depth= 1] . ( 32 sec) [ -15120.2784] [ 3228] [depth= 1] . ( 33 sec) [ -15120.2651] [ 3228] [depth= 3] . ( 34 sec) [ -15120.2514] [ 3228] [depth= 2] . ( 34 sec) [ -15120.0254] [ 3228] [depth= 1] . ( 34 sec) [ -15119.9883] [ 3228] [depth= 1] . ( 35 sec) [ -15119.9471] [ 3228] [depth= 3] . ( 35 sec) [ -15119.8427] [ 3228] [depth= 4] . ( 35 sec) [ -15119.7873] [ 3228] [depth= 2] . ( 35 sec) [ -15119.5220] [ 3228] [depth= 2] . ( 37 sec) [ -15119.5073] [ 3228] [depth= 5] . ( 39 sec) [ -15035.9915] [Branch lengths ] . ( 46 sec) [ -15023.3863] [GTR parameters ] . ( 47 sec) [ -15023.2332] [Alpha ][ 0.597277] . ( 49 sec) [ -15020.3035] [ 3208] [depth= 1] . ( 50 sec) [ -15019.0634] [ 3207] [depth= 1] . ( 51 sec) [ -14995.8144] [ 3202] [depth= 1] . ( 51 sec) [ -14994.7322] [ 3203] [depth= 1] . ( 51 sec) [ -14993.8870] [ 3202] [depth= 1] . ( 52 sec) [ -14993.8577] [ 3202] [depth= 1] . ( 53 sec) [ -14993.7999] [ 3202] [depth= 1] . ( 58 sec) [ -14993.5270] [ 3202] [depth= 1] . ( 59 sec) [ -14993.4143] [ 3202] [depth= 4] . ( 59 sec) [ -14991.0337] [ 3202] [depth= 6] . ( 60 sec) [ -14990.6912] [ 3202] [depth= 1] . ( 60 sec) [ -14989.8541] [ 3199] [depth= 1] . ( 60 sec) [ -14976.5752] [ 3199] [depth= 2] . ( 60 sec) [ -14974.0693] [ 3197] [depth= 1] . ( 62 sec) [ -14972.1943] [ 3199] [depth= 1] . ( 63 sec) [ -14968.5201] [ 3199] [depth= 1] . ( 63 sec) [ -14968.4009] [ 3199] [depth= 1] . ( 64 sec) [ -14968.2498] [ 3199] [depth= 1] . ( 64 sec) [ -14967.9658] [ 3199] [depth= 1] . ( 64 sec) [ -14967.2608] [ 3199] [depth= 1] . ( 66 sec) [ -14967.0648] [ 3199] [depth= 1] . ( 66 sec) [ -14967.0206] [ 3199] [depth= 1] . ( 67 sec) [ -14966.9800] [ 3199] [depth= 1] . ( 78 sec) [ -14943.6598] [Branch lengths ] . ( 85 sec) [ -14942.9018] [GTR parameters ] . ( 86 sec) [ -14942.8257] [Alpha ][ 0.586344] . ( 92 sec) [ -14942.7849] [ 3199] [depth= 1] . ( 101 sec) [ -14942.7716] [ 3199] [depth= 1] . ( 107 sec) [ -14942.7290] [ 3199] [depth= 1] . ( 109 sec) [ -14942.6851] [ 3199] [depth= 1] . ( 119 sec) [ -14936.5038] [Branch lengths ] . ( 121 sec) [ -14936.4167] [GTR parameters ] . ( 122 sec) [ -14936.2961] [Alpha ][ 0.572985] . ( 141 sec) [ -14936.2290] [ 3199] [depth= 1] . ( 156 sec) [ -14934.4109] [Branch lengths ] . ( 165 sec) [ -14934.3735] [GTR parameters ] . ( 166 sec) [ -14934.3507] [Alpha ][ 0.567045] . ( 195 sec) [ -14933.7831] [Branch lengths ] . ( 270 sec) [ -14933.5618] [ 3208] [depth= 2] . ( 342 sec) [ -14931.9558] [Branch lengths ] . ( 345 sec) [ -14931.9405] [GTR parameters ] . ( 345 sec) [ -14931.9383] [Alpha ][ 0.565185] . ( 501 sec) [ -14931.3376] [Branch lengths ] . ( 501 sec) [ -14931.3376] [Topology ] . ( 504 sec) [ -14927.9236] [Topology ] . ( 508 sec) [ -14923.7012] [Topology ] . ( 511 sec) [ -14922.9675] [Topology ] . ( 515 sec) [ -14922.6749] [Topology ] . ( 518 sec) [ -14922.5082] [Topology ] . ( 521 sec) [ -14922.4075] [Topology ] . ( 525 sec) [ -14922.3455] [Topology ] . ( 531 sec) [ -14922.3292] [GTR parameters ] . ( 531 sec) [ -14922.3269] [Alpha ][ 0.566996] . ( 531 sec) [ -14922.3269] [Topology ] . ( 535 sec) [ -14922.2878] [Topology ] . ( 538 sec) [ -14922.2642] [Topology ] . ( 541 sec) [ -14922.2500] [Topology ] . ( 545 sec) [ -14922.2413] [Topology ] . ( 548 sec) [ -14922.2361] [Topology ] . ( 552 sec) [ -14922.2329] [Topology ] . ( 553 sec) [ -14922.2329] [GTR parameters ] . ( 553 sec) [ -14922.2328] [Alpha ][ 0.567563] . ( 553 sec) [ -14922.2328] [Topology ] . ( 556 sec) [ -14922.2308] [Topology ] . ( 560 sec) [ -14922.2296] [Topology ] . ( 563 sec) [ -14922.2288] [Topology ] . ( 565 sec) [ -14922.2284] [GTR parameters ] . ( 565 sec) [ -14922.2284] [Alpha ][ 0.567563] . ( 565 sec) [ -14922.2284] [Topology ] . ( 568 sec) [ -14922.2279] [Topology ] . ( 569 sec) [ -14922.2279] [GTR parameters ] . ( 570 sec) [ -14922.2279] [Alpha ][ 0.567563] . Checking for NNIs, optimizing five branches... . ( 618 sec) [ -14921.3326] [Topology ] . Checking for NNIs, optimizing five branches... . ( 674 sec) [ -14921.3324] [Topology ] . Checking for NNIs, optimizing five branches... . ( 729 sec) [ -14921.3315] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14921.331478. . Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'... . Time used 0h13m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 691.31user 0.00system 13:03.18elapsed 88%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps