.......................... 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)... . ( 7 sec) [ -15465.7212] [GTR parameters ] . ( 8 sec) [ -15431.9484] [Alpha ][ 0.613860] . ( 8 sec) [ -15431.3316] [ 3250] [depth= 1] . ( 10 sec) [ -15430.9760] [ 3252] [depth= 1] . ( 11 sec) [ -15430.5960] [ 3255] [depth= 1] . ( 11 sec) [ -15402.3780] [ 3252] [depth= 1] . ( 11 sec) [ -15387.4679] [ 3269] [depth= 1] . ( 11 sec) [ -15376.8933] [ 3271] [depth= 1] . ( 12 sec) [ -15368.7103] [ 3289] [depth= 2] . ( 13 sec) [ -15360.7370] [ 3290] [depth= 1] . ( 14 sec) [ -15342.9301] [ 3286] [depth= 1] . ( 14 sec) [ -15342.2817] [ 3286] [depth= 1] . ( 15 sec) [ -15337.1367] [ 3286] [depth= 1] . ( 15 sec) [ -15328.5284] [ 3286] [depth= 1] . ( 15 sec) [ -15324.4261] [ 3286] [depth= 2] . ( 15 sec) [ -15299.4630] [ 3260] [depth= 2] . ( 16 sec) [ -15297.9546] [ 3260] [depth= 1] . ( 16 sec) [ -15226.6796] [ 3246] [depth= 2] . ( 16 sec) [ -15223.5302] [ 3246] [depth= 1] . ( 17 sec) [ -15219.9536] [ 3249] [depth= 1] . ( 17 sec) [ -15218.0654] [ 3246] [depth= 1] . ( 18 sec) [ -15215.1312] [ 3242] [depth= 1] . ( 18 sec) [ -15207.1548] [ 3241] [depth= 1] . ( 19 sec) [ -15178.2131] [ 3238] [depth= 1] . ( 19 sec) [ -15177.5438] [ 3238] [depth= 1] . ( 19 sec) [ -15176.6334] [ 3238] [depth= 1] . ( 19 sec) [ -15176.6148] [ 3238] [depth= 5] . ( 20 sec) [ -15174.4771] [ 3238] [depth= 7] . ( 21 sec) [ -15169.9818] [ 3237] [depth= 5] . ( 21 sec) [ -15168.4855] [ 3237] [depth= 3] . ( 21 sec) [ -15159.0500] [ 3237] [depth= 1] . ( 21 sec) [ -15152.2342] [ 3236] [depth= 1] . ( 22 sec) [ -15149.8557] [ 3237] [depth= 3] . ( 22 sec) [ -15149.4975] [ 3237] [depth= 2] . ( 23 sec) [ -15149.1815] [ 3237] [depth= 2] . ( 24 sec) [ -15144.5080] [ 3237] [depth= 1] . ( 24 sec) [ -15144.2312] [ 3236] [depth= 2] . ( 25 sec) [ -15141.4441] [ 3236] [depth= 4] . ( 26 sec) [ -15138.9343] [ 3236] [depth= 3] . ( 26 sec) [ -15137.4369] [ 3237] [depth= 2] . ( 26 sec) [ -15134.6409] [ 3240] [depth= 1] . ( 27 sec) [ -15125.1651] [ 3247] [depth= 1] . ( 27 sec) [ -15124.8924] [ 3268] [depth= 1] . ( 27 sec) [ -15121.4875] [ 3271] [depth= 1] . ( 27 sec) [ -15111.7082] [ 3268] [depth= 1] . ( 28 sec) [ -15110.3915] [ 3259] [depth= 1] . ( 29 sec) [ -15110.3108] [ 3259] [depth= 1] . ( 29 sec) [ -15106.8144] [ 3267] [depth= 1] . ( 30 sec) [ -15104.1425] [ 3268] [depth= 1] . ( 30 sec) [ -15089.5291] [ 3266] [depth= 1] . ( 31 sec) [ -15087.3993] [ 3266] [depth= 1] . ( 31 sec) [ -15086.2127] [ 3267] [depth= 1] . ( 32 sec) [ -15075.8849] [ 3255] [depth= 2] . ( 32 sec) [ -15074.6378] [ 3256] [depth= 1] . ( 36 sec) [ -15072.7604] [ 3256] [depth= 1] . ( 37 sec) [ -15072.6756] [ 3256] [depth= 1] . ( 40 sec) [ -15071.9309] [ 3255] [depth= 2] . ( 42 sec) [ -15066.7065] [ 3254] [depth= 4] . ( 42 sec) [ -15066.6527] [ 3254] [depth= 2] . ( 43 sec) [ -15066.6317] [ 3254] [depth= 3] . ( 44 sec) [ -15066.4662] [ 3254] [depth= 1] . ( 44 sec) [ -15066.4475] [ 3254] [depth= 2] . ( 45 sec) [ -15065.8339] [ 3254] [depth= 2] . ( 46 sec) [ -15065.7142] [ 3254] [depth= 2] . ( 49 sec) [ -15065.4899] [ 3254] [depth= 2] . ( 49 sec) [ -15065.4663] [ 3254] [depth= 1] . ( 50 sec) [ -15065.4080] [ 3254] [depth= 2] . ( 52 sec) [ -15065.3606] [ 3254] [depth= 5] . ( 57 sec) [ -14985.5307] [Branch lengths ] . ( 66 sec) [ -14972.2412] [GTR parameters ] . ( 66 sec) [ -14972.0099] [Alpha ][ 0.593758] . ( 67 sec) [ -14971.2118] [ 3252] [depth= 1] . ( 69 sec) [ -14969.6020] [ 3242] [depth= 1] . ( 70 sec) [ -14964.8776] [ 3239] [depth= 1] . ( 71 sec) [ -14963.6740] [ 3215] [depth= 1] . ( 71 sec) [ -14955.9309] [ 3219] [depth= 2] . ( 74 sec) [ -14955.9034] [ 3219] [depth= 1] . ( 74 sec) [ -14955.8487] [ 3219] [depth= 1] . ( 84 sec) [ -14955.8278] [ 3219] [depth= 2] . ( 88 sec) [ -14955.7823] [ 3219] [depth= 1] . ( 89 sec) [ -14955.5209] [ 3219] [depth= 1] . ( 90 sec) [ -14953.5216] [ 3219] [depth= 2] . ( 90 sec) [ -14953.4906] [ 3219] [depth= 5] . ( 93 sec) [ -14952.2332] [ 3216] [depth= 1] . ( 97 sec) [ -14949.0679] [ 3216] [depth= 1] . ( 97 sec) [ -14949.0018] [ 3216] [depth= 1] . ( 97 sec) [ -14948.7168] [ 3216] [depth= 1] . ( 98 sec) [ -14948.6794] [ 3216] [depth= 1] . ( 101 sec) [ -14948.4115] [ 3216] [depth= 1] . ( 101 sec) [ -14948.2911] [ 3216] [depth= 1] . ( 108 sec) [ -14948.1888] [ 3216] [depth= 1] . ( 129 sec) [ -14936.0711] [Branch lengths ] . ( 134 sec) [ -14935.1236] [GTR parameters ] . ( 135 sec) [ -14935.0638] [Alpha ][ 0.583612] . ( 141 sec) [ -14935.0222] [ 3216] [depth= 1] . ( 147 sec) [ -14935.0078] [ 3216] [depth= 2] . ( 151 sec) [ -14934.9974] [ 3216] [depth= 3] . ( 196 sec) [ -14932.5067] [Branch lengths ] . ( 201 sec) [ -14932.4659] [GTR parameters ] . ( 202 sec) [ -14932.4100] [Alpha ][ 0.574091] . ( 264 sec) [ -14931.9789] [Branch lengths ] . ( 289 sec) [ -14930.9015] [ 3215] [depth= 2] . ( 334 sec) [ -14929.9518] [ 3224] [depth= 2] . ( 405 sec) [ -14928.7571] [Branch lengths ] . ( 411 sec) [ -14928.7327] [GTR parameters ] . ( 411 sec) [ -14928.7187] [Alpha ][ 0.569395] . ( 554 sec) [ -14928.6317] [Branch lengths ] . ( 554 sec) [ -14928.6317] [Topology ] . ( 558 sec) [ -14928.2402] [Topology ] . ( 561 sec) [ -14926.2670] [Topology ] . ( 565 sec) [ -14922.4720] [Topology ] . ( 568 sec) [ -14921.7838] [Topology ] . ( 571 sec) [ -14921.6095] [Topology ] . ( 575 sec) [ -14921.5273] [Topology ] . ( 576 sec) [ -14921.5272] [GTR parameters ] . ( 577 sec) [ -14921.5249] [Alpha ][ 0.567474] . ( 577 sec) [ -14921.5249] [Topology ] . ( 580 sec) [ -14921.4776] [Topology ] . ( 584 sec) [ -14921.4501] [Topology ] . ( 587 sec) [ -14921.4344] [Topology ] . ( 590 sec) [ -14921.4271] [Topology ] . ( 594 sec) [ -14921.4301] [Topology ] . Moving backward . ( 594 sec) [ -14921.4225] [Topology ] . ( 597 sec) [ -14921.4202] [Topology ] . ( 599 sec) [ -14921.4201] [GTR parameters ] . ( 599 sec) [ -14921.4201] [Alpha ][ 0.567474] . ( 599 sec) [ -14921.4201] [Topology ] . ( 603 sec) [ -14921.4253] [Topology ] . Moving backward . ( 603 sec) [ -14921.4171] [Topology ] . ( 606 sec) [ -14921.4168] [Topology ] . ( 610 sec) [ -14921.4126] [GTR parameters ] . ( 610 sec) [ -14921.4126] [Alpha ][ 0.567474] . ( 610 sec) [ -14921.4126] [Topology ] . ( 614 sec) [ -14921.4180] [Topology ] . Moving backward . ( 614 sec) [ -14921.4104] [Topology ] . ( 617 sec) [ -14921.4109] [Topology ] . ( 619 sec) [ -14921.4109] [GTR parameters ] . ( 619 sec) [ -14921.4109] [Alpha ][ 0.567474] . ( 619 sec) [ -14921.4109] [Topology ] . ( 623 sec) [ -14921.4162] [Topology ] . Moving backward . ( 623 sec) [ -14921.4093] [Topology ] . ( 627 sec) [ -14921.4101] [Topology ] . ( 628 sec) [ -14921.4100] [GTR parameters ] . ( 628 sec) [ -14921.4100] [Alpha ][ 0.567474] . Checking for NNIs, optimizing five branches... . ( 660 sec) [ -14921.3056] [Topology ] . Checking for NNIs, optimizing five branches... . ( 691 sec) [ -14921.3024] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14921.302358. . Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'... . Time used 0h12m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 721.50user 0.00system 12:03.72elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps