.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2786_104x1051_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 717 patterns found. (out of a total of 1051 sites) . 402 sites without polymorphism (38.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -16171.4937] [GTR parameters ] . ( 6 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 7 sec) [ -16051.9734] [ 3233] [depth= 1] . ( 7 sec) [ -16044.4728] [ 3239] [depth= 1] . ( 7 sec) [ -16041.2101] [ 3233] [depth= 1] . ( 7 sec) [ -16031.8120] [ 3236] [depth= 1] . ( 8 sec) [ -16011.4895] [ 3239] [depth= 2] . ( 8 sec) [ -16011.3510] [ 3251] [depth= 2] . ( 9 sec) [ -16002.2772] [ 3253] [depth= 1] . ( 9 sec) [ -15994.3577] [ 3257] [depth= 2] . ( 9 sec) [ -15992.1697] [ 3252] [depth= 2] . ( 9 sec) [ -15990.1296] [ 3256] [depth= 1] . ( 9 sec) [ -15986.2747] [ 3253] [depth= 1] . ( 10 sec) [ -15977.1070] [ 3251] [depth= 1] . ( 11 sec) [ -15973.2771] [ 3237] [depth= 1] . ( 11 sec) [ -15962.2787] [ 3234] [depth= 1] . ( 11 sec) [ -15961.2844] [ 3238] [depth= 1] . ( 11 sec) [ -15934.6332] [ 3238] [depth= 1] . ( 12 sec) [ -15926.3319] [ 3233] [depth= 1] . ( 12 sec) [ -15926.1471] [ 3237] [depth= 2] . ( 12 sec) [ -15894.8668] [ 3228] [depth= 4] . ( 13 sec) [ -15891.4821] [ 3232] [depth= 1] . ( 13 sec) [ -15890.0526] [ 3234] [depth= 2] . ( 13 sec) [ -15888.1122] [ 3228] [depth= 1] . ( 13 sec) [ -15869.6602] [ 3219] [depth= 1] . ( 14 sec) [ -15868.3150] [ 3222] [depth= 1] . ( 14 sec) [ -15859.4357] [ 3218] [depth= 1] . ( 15 sec) [ -15857.6811] [ 3213] [depth= 1] . ( 15 sec) [ -15856.8559] [ 3212] [depth= 1] . ( 15 sec) [ -15850.7281] [ 3215] [depth= 2] . ( 15 sec) [ -15850.6540] [ 3215] [depth= 1] . ( 16 sec) [ -15848.4548] [ 3213] [depth= 3] . ( 16 sec) [ -15847.6184] [ 3213] [depth= 3] . ( 16 sec) [ -15842.3468] [ 3212] [depth= 3] . ( 17 sec) [ -15840.1403] [ 3211] [depth= 1] . ( 17 sec) [ -15838.9389] [ 3211] [depth= 1] . ( 18 sec) [ -15838.9216] [ 3213] [depth= 1] . ( 18 sec) [ -15837.5423] [ 3211] [depth= 2] . ( 18 sec) [ -15836.2600] [ 3210] [depth= 1] . ( 20 sec) [ -15835.9759] [ 3211] [depth= 1] . ( 21 sec) [ -15832.9401] [ 3210] [depth= 1] . ( 22 sec) [ -15829.5869] [ 3210] [depth= 1] . ( 26 sec) [ -15829.1001] [ 3207] [depth= 1] . ( 27 sec) [ -15828.0095] [ 3209] [depth= 1] . ( 27 sec) [ -15825.9446] [ 3209] [depth= 1] . ( 28 sec) [ -15824.7571] [ 3209] [depth= 1] . ( 28 sec) [ -15819.9096] [ 3210] [depth= 1] . ( 29 sec) [ -15819.3978] [ 3210] [depth= 1] . ( 30 sec) [ -15818.9106] [ 3210] [depth= 1] . ( 30 sec) [ -15810.4986] [ 3210] [depth= 1] . ( 30 sec) [ -15810.0893] [ 3209] [depth= 1] . ( 31 sec) [ -15809.8308] [ 3209] [depth= 1] . ( 32 sec) [ -15809.6352] [ 3211] [depth= 1] . ( 33 sec) [ -15809.1639] [ 3211] [depth= 1] . ( 33 sec) [ -15809.0293] [ 3208] [depth= 1] . ( 33 sec) [ -15808.8563] [ 3207] [depth= 1] . ( 36 sec) [ -15805.7668] [ 3206] [depth= 1] . ( 36 sec) [ -15804.8210] [ 3206] [depth= 1] . ( 36 sec) [ -15804.2174] [ 3206] [depth= 1] . ( 37 sec) [ -15803.8278] [ 3206] [depth= 1] . ( 38 sec) [ -15803.3799] [ 3207] [depth= 3] . ( 38 sec) [ -15802.1832] [ 3207] [depth= 1] . ( 38 sec) [ -15802.0612] [ 3207] [depth= 1] . ( 39 sec) [ -15801.8047] [ 3208] [depth= 1] . ( 40 sec) [ -15801.6389] [ 3207] [depth= 3] . ( 42 sec) [ -15801.0621] [ 3207] [depth= 2] . ( 43 sec) [ -15799.8267] [ 3207] [depth= 1] . ( 43 sec) [ -15796.3603] [ 3208] [depth= 2] . ( 44 sec) [ -15795.9391] [ 3208] [depth= 1] . ( 44 sec) [ -15795.8642] [ 3208] [depth= 1] . ( 44 sec) [ -15795.5001] [ 3208] [depth= 1] . ( 45 sec) [ -15795.4702] [ 3208] [depth= 1] . ( 46 sec) [ -15794.4144] [ 3208] [depth= 1] . ( 48 sec) [ -15793.6256] [ 3208] [depth= 1] . ( 49 sec) [ -15793.4448] [ 3208] [depth= 1] . ( 50 sec) [ -15793.4310] [ 3208] [depth= 1] . ( 50 sec) [ -15793.3560] [ 3208] [depth= 1] . ( 50 sec) [ -15793.2598] [ 3208] [depth= 1] . ( 51 sec) [ -15793.2068] [ 3208] [depth= 1] . ( 53 sec) [ -15701.4518] [Branch lengths ] . ( 60 sec) [ -15691.2786] [GTR parameters ] . ( 61 sec) [ -15690.6608] [Alpha ][ 0.528636] . ( 62 sec) [ -15688.7715] [ 3205] [depth= 1] . ( 62 sec) [ -15688.3912] [ 3205] [depth= 1] . ( 63 sec) [ -15687.6891] [ 3208] [depth= 1] . ( 64 sec) [ -15686.9522] [ 3208] [depth= 1] . ( 64 sec) [ -15685.9380] [ 3206] [depth= 1] . ( 67 sec) [ -15685.3836] [ 3208] [depth= 1] . ( 68 sec) [ -15683.1610] [ 3202] [depth= 2] . ( 69 sec) [ -15682.8318] [ 3203] [depth= 1] . ( 73 sec) [ -15682.6232] [ 3202] [depth= 1] . ( 104 sec) [ -15682.5115] [ 3202] [depth= 1] . ( 115 sec) [ -15668.2499] [Branch lengths ] . ( 119 sec) [ -15668.0859] [GTR parameters ] . ( 120 sec) [ -15668.0175] [Alpha ][ 0.538332] . ( 126 sec) [ -15667.9356] [ 3201] [depth= 1] . ( 176 sec) [ -15665.9925] [Branch lengths ] . ( 180 sec) [ -15665.9523] [GTR parameters ] . ( 180 sec) [ -15665.9522] [Alpha ][ 0.538870] . ( 236 sec) [ -15665.2221] [Branch lengths ] . ( 264 sec) [ -15665.2018] [ 3198] [depth= 1] . ( 380 sec) [ -15665.1883] [ 3198] [depth= 2] . ( 386 sec) [ -15664.4440] [Branch lengths ] . ( 390 sec) [ -15664.4289] [GTR parameters ] . ( 391 sec) [ -15664.4139] [Alpha ][ 0.543379] . ( 391 sec) [ -15664.4139] [Topology ] . ( 394 sec) [ -15664.0797] [Topology ] . ( 398 sec) [ -15662.9541] [Topology ] . ( 401 sec) [ -15660.9366] [Topology ] . ( 404 sec) [ -15660.5195] [Topology ] . ( 408 sec) [ -15660.4558] [Topology ] . ( 411 sec) [ -15660.4338] [Topology ] . ( 415 sec) [ -15660.4330] [GTR parameters ] . ( 415 sec) [ -15660.4301] [Alpha ][ 0.545315] . ( 415 sec) [ -15660.4301] [Topology ] . ( 418 sec) [ -15660.4171] [Topology ] . ( 422 sec) [ -15660.4087] [Topology ] . ( 425 sec) [ -15660.4028] [Topology ] . ( 429 sec) [ -15660.3985] [Topology ] . ( 432 sec) [ -15660.3953] [Topology ] . ( 436 sec) [ -15660.3930] [Topology ] . ( 438 sec) [ -15660.3925] [GTR parameters ] . ( 438 sec) [ -15660.3922] [Alpha ][ 0.545936] . ( 438 sec) [ -15660.3922] [Topology ] . ( 442 sec) [ -15660.3902] [Topology ] . ( 445 sec) [ -15660.3886] [Topology ] . ( 448 sec) [ -15660.3875] [Topology ] . ( 452 sec) [ -15660.3867] [Topology ] . ( 453 sec) [ -15660.3866] [GTR parameters ] . ( 454 sec) [ -15660.3866] [Alpha ][ 0.545936] . ( 454 sec) [ -15660.3866] [Topology ] . ( 457 sec) [ -15660.3859] [Topology ] . ( 458 sec) [ -15660.3858] [GTR parameters ] . ( 459 sec) [ -15660.3858] [Alpha ][ 0.545936] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15660.385831. . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Time used 0h8m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 481.98user 0.00system 8:06.22elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps