.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2623_139x1044_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 . Compressing sequences... . 959 patterns found. (out of a total of 1044 sites) . 202 sites without polymorphism (19.35%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 71Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 12 sec) [ -48412.0933] [GTR parameters ] . ( 13 sec) [ -47896.6604] [Alpha ][ 0.500960] . ( 14 sec) [ -47896.0418] [11967] [depth= 1] . ( 14 sec) [ -47889.7491] [11967] [depth= 1] . ( 15 sec) [ -47889.7184] [11967] [depth= 1] . ( 16 sec) [ -47884.8015] [11974] [depth= 1] . ( 16 sec) [ -47884.1065] [11967] [depth= 1] . ( 17 sec) [ -47880.9605] [11971] [depth= 1] . ( 18 sec) [ -47880.5369] [11972] [depth= 1] . ( 19 sec) [ -47774.6680] [11977] [depth= 1] . ( 20 sec) [ -47746.4842] [11974] [depth= 1] . ( 21 sec) [ -47691.9593] [11965] [depth= 10] . ( 21 sec) [ -47678.9464] [11944] [depth= 7] . ( 22 sec) [ -47669.6854] [11942] [depth= 1] . ( 23 sec) [ -47665.6354] [11947] [depth= 1] . ( 23 sec) [ -47658.1171] [11949] [depth= 1] . ( 24 sec) [ -47653.7020] [11951] [depth= 1] . ( 25 sec) [ -47638.8318] [11949] [depth= 1] . ( 25 sec) [ -47590.0596] [11932] [depth= 8] . ( 26 sec) [ -47526.5165] [11930] [depth= 2] . ( 26 sec) [ -47522.6803] [11935] [depth= 2] . ( 27 sec) [ -47520.1468] [11938] [depth= 1] . ( 27 sec) [ -47509.4594] [11924] [depth= 1] . ( 28 sec) [ -47504.1025] [11926] [depth= 1] . ( 29 sec) [ -47503.9077] [11923] [depth= 1] . ( 29 sec) [ -47435.2032] [11921] [depth= 1] . ( 30 sec) [ -47434.8112] [11919] [depth= 1] . ( 30 sec) [ -47434.0884] [11921] [depth= 1] . ( 31 sec) [ -47408.3802] [11912] [depth= 1] . ( 32 sec) [ -47406.8051] [11919] [depth= 1] . ( 32 sec) [ -47398.9314] [11917] [depth= 2] . ( 33 sec) [ -47395.1014] [11917] [depth= 1] . ( 33 sec) [ -47393.4723] [11908] [depth= 11] . ( 33 sec) [ -47322.7419] [11889] [depth= 11] . ( 34 sec) [ -47322.5987] [11890] [depth= 2] . ( 34 sec) [ -47317.0897] [11889] [depth= 2] . ( 35 sec) [ -47306.9571] [11889] [depth= 1] . ( 35 sec) [ -47296.9314] [11891] [depth= 2] . ( 36 sec) [ -47293.6942] [11892] [depth= 1] . ( 37 sec) [ -47292.2287] [11891] [depth= 1] . ( 37 sec) [ -47291.8039] [11889] [depth= 1] . ( 37 sec) [ -47291.1975] [11889] [depth= 1] . ( 38 sec) [ -47268.1630] [11883] [depth= 1] . ( 38 sec) [ -47260.3346] [11883] [depth= 1] . ( 38 sec) [ -47233.3725] [11887] [depth= 2] . ( 39 sec) [ -47220.1232] [11890] [depth= 1] . ( 39 sec) [ -47215.6834] [11884] [depth= 3] . ( 40 sec) [ -47129.5826] [11848] [depth= 10] . ( 40 sec) [ -47121.1510] [11849] [depth= 1] . ( 41 sec) [ -47119.5980] [11848] [depth= 1] . ( 41 sec) [ -47112.2688] [11840] [depth= 7] . ( 41 sec) [ -47107.3666] [11838] [depth= 2] . ( 42 sec) [ -47086.7604] [11838] [depth= 2] . ( 42 sec) [ -47060.5077] [11827] [depth= 8] . ( 43 sec) [ -47058.7698] [11818] [depth= 1] . ( 44 sec) [ -47057.6055] [11826] [depth= 1] . ( 44 sec) [ -47040.7615] [11819] [depth= 9] . ( 45 sec) [ -47040.5780] [11822] [depth= 1] . ( 46 sec) [ -47039.6206] [11824] [depth= 4] . ( 47 sec) [ -47039.3092] [11825] [depth= 4] . ( 47 sec) [ -47034.7995] [11817] [depth= 1] . ( 47 sec) [ -47029.0497] [11825] [depth= 1] . ( 48 sec) [ -47025.7197] [11827] [depth= 4] . ( 49 sec) [ -47012.8470] [11821] [depth= 9] . ( 50 sec) [ -46954.0708] [11801] [depth= 5] . ( 50 sec) [ -46930.9528] [11792] [depth= 1] . ( 51 sec) [ -46929.7693] [11791] [depth= 2] . ( 51 sec) [ -46929.1534] [11795] [depth= 1] . ( 52 sec) [ -46927.0353] [11794] [depth= 1] . ( 53 sec) [ -46923.5160] [11795] [depth= 1] . ( 53 sec) [ -46918.5777] [11796] [depth= 1] . ( 54 sec) [ -46916.9645] [11795] [depth= 2] . ( 54 sec) [ -46911.5131] [11789] [depth= 1] . ( 54 sec) [ -46903.2673] [11788] [depth= 2] . ( 55 sec) [ -46900.6212] [11792] [depth= 1] . ( 56 sec) [ -46898.1654] [11790] [depth= 3] . ( 57 sec) [ -46897.1996] [11793] [depth= 1] . ( 57 sec) [ -46893.8600] [11790] [depth= 2] . ( 58 sec) [ -46893.6068] [11793] [depth= 1] . ( 60 sec) [ -46886.2323] [11797] [depth= 1] . ( 61 sec) [ -46880.9043] [11793] [depth= 1] . ( 62 sec) [ -46878.7707] [11789] [depth= 1] . ( 62 sec) [ -46876.1304] [11788] [depth= 3] . ( 63 sec) [ -46873.5800] [11786] [depth= 3] . ( 63 sec) [ -46873.5416] [11783] [depth= 1] . ( 64 sec) [ -46868.6886] [11791] [depth= 1] . ( 64 sec) [ -46856.4919] [11783] [depth= 1] . ( 64 sec) [ -46854.0401] [11787] [depth= 1] . ( 65 sec) [ -46851.9353] [11787] [depth= 2] . ( 66 sec) [ -46849.5299] [11792] [depth= 2] . ( 66 sec) [ -46835.0678] [11792] [depth= 1] . ( 67 sec) [ -46834.9489] [11790] [depth= 2] . ( 67 sec) [ -46834.5417] [11788] [depth= 1] . ( 68 sec) [ -46821.2412] [11784] [depth= 1] . ( 68 sec) [ -46817.2874] [11781] [depth= 1] . ( 69 sec) [ -46815.8002] [11781] [depth= 1] . ( 70 sec) [ -46809.8727] [11785] [depth= 1] . ( 70 sec) [ -46809.2413] [11786] [depth= 2] . ( 71 sec) [ -46807.2359] [11789] [depth= 1] . ( 71 sec) [ -46799.5849] [11780] [depth= 2] . ( 73 sec) [ -46791.5239] [11784] [depth= 1] . ( 74 sec) [ -46785.9409] [11781] [depth= 3] . ( 74 sec) [ -46783.5217] [11783] [depth= 1] . ( 75 sec) [ -46783.1387] [11781] [depth= 1] . ( 77 sec) [ -46779.9018] [11786] [depth= 1] . ( 77 sec) [ -46777.8240] [11781] [depth= 1] . ( 78 sec) [ -46770.6025] [11778] [depth= 1] . ( 78 sec) [ -46756.5826] [11779] [depth= 1] . ( 78 sec) [ -46748.1042] [11781] [depth= 1] . ( 79 sec) [ -46718.7961] [11781] [depth= 1] . ( 79 sec) [ -46702.6952] [11777] [depth= 1] . ( 79 sec) [ -46686.1965] [11776] [depth= 4] . ( 80 sec) [ -46685.9180] [11778] [depth= 1] . ( 80 sec) [ -46683.5880] [11774] [depth= 1] . ( 81 sec) [ -46681.9225] [11773] [depth= 2] . ( 81 sec) [ -46672.5150] [11764] [depth= 1] . ( 82 sec) [ -46669.2363] [11761] [depth= 2] . ( 82 sec) [ -46666.2447] [11760] [depth= 1] . ( 83 sec) [ -46665.1375] [11757] [depth= 4] . ( 83 sec) [ -46660.9781] [11758] [depth= 1] . ( 83 sec) [ -46640.3396] [11761] [depth= 1] . ( 84 sec) [ -46622.5552] [11765] [depth= 1] . ( 85 sec) [ -46621.7140] [11770] [depth= 1] . ( 85 sec) [ -46616.0759] [11765] [depth= 1] . ( 85 sec) [ -46598.5865] [11757] [depth= 2] . ( 85 sec) [ -46593.6260] [11758] [depth= 1] . ( 86 sec) [ -46591.2225] [11758] [depth= 1] . ( 86 sec) [ -46588.8665] [11757] [depth= 1] . ( 87 sec) [ -46574.6584] [11758] [depth= 1] . ( 88 sec) [ -46571.8866] [11762] [depth= 1] . ( 88 sec) [ -46569.8995] [11758] [depth= 1] . ( 90 sec) [ -46569.8870] [11760] [depth= 1] . ( 91 sec) [ -46568.3421] [11759] [depth= 1] . ( 91 sec) [ -46567.7925] [11760] [depth= 3] . ( 92 sec) [ -46566.2911] [11759] [depth= 2] . ( 92 sec) [ -46565.7276] [11761] [depth= 1] . ( 93 sec) [ -46562.5362] [11761] [depth= 1] . ( 93 sec) [ -46561.5999] [11759] [depth= 1] . ( 93 sec) [ -46559.9442] [11761] [depth= 2] . ( 94 sec) [ -46555.7153] [11762] [depth= 1] . ( 95 sec) [ -46550.4855] [11762] [depth= 2] . ( 95 sec) [ -46550.3427] [11759] [depth= 2] . ( 95 sec) [ -46549.7750] [11757] [depth= 1] . ( 96 sec) [ -46547.5104] [11759] [depth= 1] . ( 96 sec) [ -46547.2786] [11760] [depth= 1] . ( 98 sec) [ -46286.4111] [Branch lengths ] . ( 107 sec) [ -46239.2082] [GTR parameters ] . ( 108 sec) [ -46239.0351] [Alpha ][ 0.492531] . ( 109 sec) [ -46238.1935] [11760] [depth= 1] . ( 110 sec) [ -46237.9999] [11765] [depth= 1] . ( 111 sec) [ -46234.2504] [11767] [depth= 1] . ( 114 sec) [ -46226.1767] [11761] [depth= 1] . ( 115 sec) [ -46212.5414] [11746] [depth= 5] . ( 116 sec) [ -46211.4208] [11738] [depth= 6] . ( 119 sec) [ -46203.3408] [11739] [depth= 6] . ( 121 sec) [ -46194.1187] [11735] [depth= 6] . ( 122 sec) [ -46193.4564] [11731] [depth= 1] . ( 124 sec) [ -46193.4316] [11731] [depth= 2] . ( 130 sec) [ -46193.0118] [11728] [depth= 2] . ( 131 sec) [ -46190.4188] [11718] [depth= 6] . ( 131 sec) [ -46189.5225] [11716] [depth= 1] . ( 132 sec) [ -46183.2468] [11710] [depth= 8] . ( 134 sec) [ -46177.9005] [11706] [depth= 2] . ( 135 sec) [ -46176.1522] [11705] [depth= 3] . ( 136 sec) [ -46174.7361] [11707] [depth= 1] . ( 138 sec) [ -46173.7610] [11707] [depth= 2] . ( 138 sec) [ -46169.1084] [11698] [depth= 3] . ( 141 sec) [ -46168.0396] [11702] [depth= 3] . ( 141 sec) [ -46167.2814] [11702] [depth= 2] . ( 142 sec) [ -46166.9918] [11700] [depth= 2] . ( 142 sec) [ -46164.9527] [11700] [depth= 2] . ( 143 sec) [ -46162.7533] [11703] [depth= 1] . ( 145 sec) [ -46161.5908] [11702] [depth= 1] . ( 148 sec) [ -46159.7393] [11704] [depth= 1] . ( 150 sec) [ -46159.4914] [11705] [depth= 1] . ( 155 sec) [ -46158.3994] [11707] [depth= 3] . ( 157 sec) [ -46157.8064] [11711] [depth= 1] . ( 158 sec) [ -46157.7827] [11709] [depth= 1] . ( 160 sec) [ -46157.4320] [11713] [depth= 1] . ( 160 sec) [ -46157.1097] [11712] [depth= 1] . ( 162 sec) [ -46156.4321] [11710] [depth= 2] . ( 164 sec) [ -46154.3376] [11713] [depth= 1] . ( 166 sec) [ -46152.7799] [11713] [depth= 1] . ( 168 sec) [ -46152.3236] [11718] [depth= 1] . ( 169 sec) [ -46151.3614] [11721] [depth= 1] . ( 170 sec) [ -46150.6616] [11718] [depth= 1] . ( 171 sec) [ -46149.6522] [11721] [depth= 1] . ( 172 sec) [ -46147.5609] [11716] [depth= 1] . ( 176 sec) [ -46074.6548] [Branch lengths ] . ( 183 sec) [ -46071.6534] [GTR parameters ] . ( 184 sec) [ -46070.1542] [Alpha ][ 0.515258] . ( 185 sec) [ -46069.8580] [11716] [depth= 1] . ( 185 sec) [ -46069.5146] [11714] [depth= 1] . ( 186 sec) [ -46069.4072] [11716] [depth= 1] . ( 195 sec) [ -46067.8342] [11717] [depth= 6] . ( 197 sec) [ -46067.3688] [11714] [depth= 1] . ( 201 sec) [ -46067.3454] [11714] [depth= 2] . ( 205 sec) [ -46067.0657] [11719] [depth= 1] . ( 206 sec) [ -46066.7667] [11720] [depth= 1] . ( 207 sec) [ -46066.6845] [11719] [depth= 1] . ( 213 sec) [ -46066.5830] [11721] [depth= 1] . ( 216 sec) [ -46059.0482] [11723] [depth= 6] . ( 216 sec) [ -46058.9198] [11723] [depth= 1] . ( 221 sec) [ -46058.8770] [11719] [depth= 1] . ( 228 sec) [ -46058.3983] [11722] [depth= 3] . ( 233 sec) [ -46057.1442] [11722] [depth= 1] . ( 236 sec) [ -46056.6222] [11727] [depth= 1] . ( 238 sec) [ -46055.7265] [11722] [depth= 1] . ( 239 sec) [ -46050.7903] [11718] [depth= 1] . ( 245 sec) [ -46050.5994] [11718] [depth= 1] . ( 245 sec) [ -46050.4476] [11719] [depth= 1] . ( 249 sec) [ -46046.3788] [11721] [depth= 2] . ( 255 sec) [ -46046.1548] [11722] [depth= 1] . ( 255 sec) [ -46045.4089] [11727] [depth= 1] . ( 258 sec) [ -46009.3312] [Branch lengths ] . ( 265 sec) [ -46008.5662] [GTR parameters ] . ( 266 sec) [ -46008.0436] [Alpha ][ 0.528324] . ( 267 sec) [ -46007.8876] [11727] [depth= 1] . ( 289 sec) [ -46007.6337] [11728] [depth= 1] . ( 300 sec) [ -46007.5380] [11725] [depth= 1] . ( 344 sec) [ -45992.9999] [Branch lengths ] . ( 349 sec) [ -45992.7388] [GTR parameters ] . ( 349 sec) [ -45992.6961] [Alpha ][ 0.531950] . ( 350 sec) [ -45992.6301] [11725] [depth= 1] . ( 373 sec) [ -45992.3213] [11729] [depth= 2] . ( 431 sec) [ -45986.2281] [Branch lengths ] . ( 438 sec) [ -45986.0998] [GTR parameters ] . ( 438 sec) [ -45986.0998] [Alpha ][ 0.531950] . ( 439 sec) [ -45986.0760] [11729] [depth= 1] . ( 447 sec) [ -45919.5415] [11746] [depth= 14] . ( 449 sec) [ -45919.0363] [11755] [depth= 1] . ( 451 sec) [ -45918.5898] [11761] [depth= 1] . ( 517 sec) [ -45911.9589] [Branch lengths ] . ( 523 sec) [ -45911.5804] [GTR parameters ] . ( 524 sec) [ -45911.5450] [Alpha ][ 0.534885] . ( 534 sec) [ -45911.4020] [11755] [depth= 1] . ( 603 sec) [ -45908.8496] [Branch lengths ] . ( 604 sec) [ -45908.8302] [GTR parameters ] . ( 605 sec) [ -45908.8266] [Alpha ][ 0.535752] . ( 684 sec) [ -45907.9116] [Branch lengths ] . ( 688 sec) [ -45906.9405] [11757] [depth= 1] . ( 702 sec) [ -45901.2874] [11862] [depth= 8] . ( 713 sec) [ -45898.4243] [11886] [depth= 6] . ( 726 sec) [ -45897.3031] [11973] [depth= 4] . ( 739 sec) [ -45896.7487] [11966] [depth= 1] . ( 764 sec) [ -45896.6851] [11961] [depth= 6] . ( 792 sec) [ -45896.2109] [11961] [depth= 1] . ( 874 sec) [ -45894.9374] [11961] [depth= 1] . ( 902 sec) [ -45894.5000] [11965] [depth= 1] . ( 907 sec) [ -45894.1600] [11961] [depth= 1] . ( 911 sec) [ -45892.6795] [11959] [depth= 2] . ( 939 sec) [ -45884.7326] [Branch lengths ] . ( 947 sec) [ -45884.4536] [GTR parameters ] . ( 947 sec) [ -45884.2199] [Alpha ][ 0.527707] . ( 965 sec) [ -45882.7577] [11965] [depth= 1] . ( 966 sec) [ -45880.0747] [11939] [depth= 1] . ( 1162 sec) [ -45879.9974] [11943] [depth= 1] . ( 1167 sec) [ -45879.8872] [11939] [depth= 1] . ( 1198 sec) [ -45877.2060] [Branch lengths ] . ( 1203 sec) [ -45877.1917] [GTR parameters ] . ( 1204 sec) [ -45877.1900] [Alpha ][ 0.528410] . ( 1223 sec) [ -45863.9410] [11881] [depth= 3] . ( 1458 sec) [ -45863.0162] [Branch lengths ] . ( 1463 sec) [ -45863.0016] [GTR parameters ] . ( 1464 sec) [ -45862.8792] [Alpha ][ 0.534397] . ( 1482 sec) [ -45862.6956] [11877] [depth= 1] . ( 1719 sec) [ -45862.1857] [Branch lengths ] . ( 1723 sec) [ -45862.1793] [GTR parameters ] . ( 1724 sec) [ -45862.1792] [Alpha ][ 0.535180] . ( 1724 sec) [ -45862.1792] [Topology ] . ( 1729 sec) [ -45862.0868] [Topology ] . ( 1735 sec) [ -45862.0568] [Topology ] . ( 1740 sec) [ -45862.0422] [Topology ] . ( 1746 sec) [ -45862.0343] [Topology ] . ( 1751 sec) [ -45862.0297] [Topology ] . ( 1757 sec) [ -45862.0268] [Topology ] . ( 1758 sec) [ -45862.0263] [GTR parameters ] . ( 1759 sec) [ -45862.0261] [Alpha ][ 0.534645] . ( 1759 sec) [ -45862.0261] [Topology ] . ( 1765 sec) [ -45862.0239] [Topology ] . ( 1770 sec) [ -45862.0225] [Topology ] . ( 1776 sec) [ -45862.0214] [Topology ] . ( 1781 sec) [ -45862.0206] [Topology ] . ( 1783 sec) [ -45862.0200] [GTR parameters ] . ( 1783 sec) [ -45862.0200] [Alpha ][ 0.534645] . ( 1784 sec) [ -45862.0200] [Topology ] . ( 1789 sec) [ -45862.0193] [Topology ] . ( 1790 sec) [ -45862.0193] [GTR parameters ] . ( 1791 sec) [ -45862.0193] [Alpha ][ 0.534645] . Checking for NNIs, optimizing five branches... . ( 1843 sec) [ -45861.8842] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1896 sec) [ -45861.8069] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1948 sec) [ -45861.7437] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2000 sec) [ -45861.0256] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -45861.025631. . Printing the most likely tree in file 'nucleic_M2623_139x1044_2006.phy_phyml_tree.txt'... . Time used 0h34m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2043.74user 0.00system 34:17.29elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps