.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_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... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17550.8937] [GTR parameters ] . ( 1 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 3 sec) [ -17215.2819] [ 3954] [depth= 1] . ( 3 sec) [ -17212.5717] [ 3953] [depth= 1] . ( 3 sec) [ -17211.0309] [ 3956] [depth= 1] . ( 3 sec) [ -17210.9694] [ 3957] [depth= 1] . ( 12 sec) [ -17209.0242] [ 3961] [depth= 2] . ( 12 sec) [ -17208.2432] [ 3961] [depth= 2] . ( 12 sec) [ -17196.5597] [ 3953] [depth= 1] . ( 13 sec) [ -17188.0135] [ 3961] [depth= 1] . ( 14 sec) [ -17184.8034] [ 3953] [depth= 1] . ( 26 sec) [ -17184.4774] [ 3952] [depth= 3] . ( 27 sec) [ -17180.2228] [ 3953] [depth= 3] . ( 28 sec) [ -17179.3468] [ 3953] [depth= 1] . ( 28 sec) [ -17179.0051] [ 3953] [depth= 1] . ( 29 sec) [ -17178.8158] [ 3953] [depth= 1] . ( 29 sec) [ -17176.6913] [ 3952] [depth= 2] . ( 33 sec) [ -17168.5566] [ 3951] [depth= 2] . ( 33 sec) [ -17167.3994] [ 3950] [depth= 1] . ( 33 sec) [ -17167.1345] [ 3950] [depth= 1] . ( 33 sec) [ -17167.0310] [ 3950] [depth= 1] . ( 35 sec) [ -17166.8838] [ 3950] [depth= 1] . ( 46 sec) [ -17165.5368] [ 3953] [depth= 1] . ( 46 sec) [ -17158.7180] [ 3951] [depth= 1] . ( 46 sec) [ -17158.7062] [ 3950] [depth= 1] . ( 46 sec) [ -17156.7871] [ 3952] [depth= 1] . ( 46 sec) [ -17145.0156] [ 3968] [depth= 1] . ( 46 sec) [ -17108.3955] [ 3952] [depth= 1] . ( 46 sec) [ -17104.5639] [ 3963] [depth= 2] . ( 46 sec) [ -17059.3367] [ 3955] [depth= 2] . ( 48 sec) [ -17053.1300] [ 3969] [depth= 2] . ( 50 sec) [ -17050.8595] [ 3962] [depth= 1] . ( 52 sec) [ -17044.9114] [ 3962] [depth= 1] . ( 52 sec) [ -17038.0119] [ 3962] [depth= 1] . ( 52 sec) [ -17031.8102] [ 3967] [depth= 1] . ( 52 sec) [ -17029.2964] [ 3970] [depth= 1] . ( 58 sec) [ -17028.7171] [ 3966] [depth= 1] . ( 58 sec) [ -17026.1417] [ 3970] [depth= 1] . ( 60 sec) [ -17012.7810] [ 3966] [depth= 1] . ( 60 sec) [ -17006.7888] [ 3968] [depth= 1] . ( 60 sec) [ -17006.1828] [ 3965] [depth= 1] . ( 60 sec) [ -16978.0684] [ 3964] [depth= 1] . ( 61 sec) [ -16975.4074] [ 3959] [depth= 1] . ( 62 sec) [ -16975.2268] [ 3969] [depth= 1] . ( 64 sec) [ -16968.5067] [ 3972] [depth= 1] . ( 65 sec) [ -16959.4944] [ 3972] [depth= 1] . ( 65 sec) [ -16953.8123] [ 3975] [depth= 1] . ( 67 sec) [ -16953.4926] [ 3971] [depth= 1] . ( 68 sec) [ -16906.5133] [Branch lengths ] . ( 72 sec) [ -16439.1912] [GTR parameters ] . ( 72 sec) [ -16368.6329] [Alpha ][ 0.306544] . ( 76 sec) [ -16368.2074] [ 3972] [depth= 1] . ( 85 sec) [ -16366.4787] [ 3975] [depth= 1] . ( 103 sec) [ -16366.3894] [ 3976] [depth= 1] . ( 104 sec) [ -16366.3705] [ 3976] [depth= 1] . ( 110 sec) [ -16366.3482] [ 3976] [depth= 1] . ( 110 sec) [ -16366.2883] [ 3976] [depth= 1] . ( 121 sec) [ -16357.6296] [ 3967] [depth= 1] . ( 134 sec) [ -16350.4973] [ 3959] [depth= 2] . ( 140 sec) [ -16349.0350] [ 3960] [depth= 1] . ( 141 sec) [ -16348.8253] [ 3959] [depth= 1] . ( 142 sec) [ -16346.9788] [ 3949] [depth= 1] . ( 143 sec) [ -16346.0450] [ 3946] [depth= 1] . ( 149 sec) [ -16337.2016] [ 3943] [depth= 1] . ( 153 sec) [ -16337.1029] [ 3944] [depth= 1] . ( 159 sec) [ -16337.0206] [ 3947] [depth= 1] . ( 162 sec) [ -16300.8161] [Branch lengths ] . ( 165 sec) [ -16282.5015] [GTR parameters ] . ( 165 sec) [ -16281.8929] [Alpha ][ 0.293899] . ( 167 sec) [ -16281.3510] [ 3947] [depth= 1] . ( 239 sec) [ -16280.5116] [ 3945] [depth= 1] . ( 266 sec) [ -16268.0717] [Branch lengths ] . ( 270 sec) [ -16265.4074] [GTR parameters ] . ( 270 sec) [ -16265.4053] [Alpha ][ 0.293119] . ( 372 sec) [ -16259.6347] [Branch lengths ] . ( 415 sec) [ -16258.2888] [Branch lengths ] . ( 416 sec) [ -16258.2888] [Topology ] . ( 417 sec) [ -16257.0066] [Topology ] . ( 418 sec) [ -16256.8515] [Topology ] . ( 420 sec) [ -16256.8071] [Topology ] . ( 421 sec) [ -16256.7894] [Topology ] . ( 422 sec) [ -16256.7814] [Topology ] . ( 424 sec) [ -16256.7775] [Topology ] . ( 425 sec) [ -16256.7755] [Topology ] . ( 428 sec) [ -16254.4896] [GTR parameters ] . ( 429 sec) [ -16254.4851] [Alpha ][ 0.292009] . ( 429 sec) [ -16254.4851] [Topology ] . ( 430 sec) [ -16254.0006] [Topology ] . ( 431 sec) [ -16253.8281] [Topology ] . ( 433 sec) [ -16253.7437] [Topology ] . ( 434 sec) [ -16253.7001] [Topology ] . ( 435 sec) [ -16253.6770] [Topology ] . ( 437 sec) [ -16253.6647] [Topology ] . ( 440 sec) [ -16253.4043] [GTR parameters ] . ( 440 sec) [ -16253.3907] [Alpha ][ 0.290431] . ( 440 sec) [ -16253.3907] [Topology ] . ( 441 sec) [ -16253.2983] [Topology ] . ( 442 sec) [ -16253.2620] [Topology ] . ( 444 sec) [ -16253.2434] [Topology ] . ( 445 sec) [ -16253.2335] [Topology ] . ( 447 sec) [ -16253.2282] [Topology ] . ( 448 sec) [ -16253.2253] [Topology ] . ( 452 sec) [ -16253.1632] [GTR parameters ] . ( 452 sec) [ -16253.1588] [Alpha ][ 0.289328] . ( 452 sec) [ -16253.1588] [Topology ] . ( 454 sec) [ -16253.1359] [Topology ] . ( 455 sec) [ -16253.1272] [Topology ] . ( 456 sec) [ -16253.1228] [Topology ] . ( 458 sec) [ -16253.1204] [Topology ] . ( 459 sec) [ -16253.1191] [Topology ] . ( 460 sec) [ -16253.1184] [Topology ] . ( 461 sec) [ -16253.1027] [GTR parameters ] . ( 461 sec) [ -16253.1020] [Alpha ][ 0.288834] . ( 461 sec) [ -16253.1020] [Topology ] . ( 462 sec) [ -16253.0965] [Topology ] . ( 464 sec) [ -16253.0944] [Topology ] . ( 465 sec) [ -16253.0933] [Topology ] . ( 466 sec) [ -16253.0927] [Topology ] . ( 467 sec) [ -16253.0891] [GTR parameters ] . ( 467 sec) [ -16253.0890] [Alpha ][ 0.288545] . ( 467 sec) [ -16253.0890] [Topology ] . ( 469 sec) [ -16253.0868] [Topology ] . ( 470 sec) [ -16253.0859] [Topology ] . ( 470 sec) [ -16253.0855] [GTR parameters ] . ( 470 sec) [ -16253.0855] [Alpha ][ 0.288545] . ( 470 sec) [ -16253.0855] [Topology ] . ( 472 sec) [ -16253.0846] [Topology ] . ( 473 sec) [ -16253.0842] [GTR parameters ] . ( 473 sec) [ -16253.0842] [Alpha ][ 0.288545] . ( 473 sec) [ -16253.0842] [Topology ] . ( 474 sec) [ -16253.0837] [Topology ] . ( 475 sec) [ -16253.0837] [GTR parameters ] . ( 475 sec) [ -16253.0837] [Alpha ][ 0.288545] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.083666. . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 0h8m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 474.19user 0.00system 8:08.18elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps