.......................... 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)... . ( 5 sec) [ -16171.4937] [GTR parameters ] . ( 6 sec) [ -16055.6228] [Alpha ][ 0.500960] . ( 11 sec) [ -16051.9734] [ 3233] [depth= 1] . ( 11 sec) [ -16044.4728] [ 3239] [depth= 1] . ( 11 sec) [ -16041.2101] [ 3233] [depth= 1] . ( 11 sec) [ -16031.8120] [ 3236] [depth= 1] . ( 18 sec) [ -16011.4895] [ 3239] [depth= 2] . ( 18 sec) [ -16011.3510] [ 3251] [depth= 2] . ( 18 sec) [ -16002.6634] [ 3258] [depth= 1] . ( 19 sec) [ -15999.1668] [ 3251] [depth= 1] . ( 24 sec) [ -15996.3206] [ 3261] [depth= 2] . ( 25 sec) [ -15985.9504] [ 3249] [depth= 2] . ( 25 sec) [ -15969.6564] [ 3245] [depth= 2] . ( 30 sec) [ -15965.2883] [ 3247] [depth= 1] . ( 42 sec) [ -15960.1886] [ 3249] [depth= 1] . ( 42 sec) [ -15956.9601] [ 3260] [depth= 3] . ( 42 sec) [ -15954.3312] [ 3260] [depth= 1] . ( 47 sec) [ -15951.2728] [ 3288] [depth= 2] . ( 48 sec) [ -15932.2317] [ 3266] [depth= 2] . ( 53 sec) [ -15928.3569] [ 3264] [depth= 1] . ( 54 sec) [ -15922.3121] [ 3268] [depth= 1] . ( 54 sec) [ -15912.0854] [ 3253] [depth= 2] . ( 54 sec) [ -15911.4756] [ 3258] [depth= 1] . ( 55 sec) [ -15904.2178] [ 3249] [depth= 2] . ( 55 sec) [ -15893.7390] [ 3240] [depth= 1] . ( 58 sec) [ -15890.0941] [ 3252] [depth= 1] . ( 58 sec) [ -15889.4654] [ 3251] [depth= 1] . ( 59 sec) [ -15883.8538] [ 3246] [depth= 2] . ( 59 sec) [ -15860.2128] [ 3236] [depth= 1] . ( 68 sec) [ -15854.0858] [ 3238] [depth= 2] . ( 72 sec) [ -15850.5279] [ 3231] [depth= 1] . ( 73 sec) [ -15850.3690] [ 3238] [depth= 1] . ( 101 sec) [ -15847.3373] [ 3231] [depth= 1] . ( 101 sec) [ -15847.1128] [ 3242] [depth= 1] . ( 102 sec) [ -15832.5276] [ 3231] [depth= 1] . ( 102 sec) [ -15830.3972] [ 3226] [depth= 1] . ( 102 sec) [ -15829.7455] [ 3225] [depth= 1] . ( 103 sec) [ -15822.6964] [ 3228] [depth= 2] . ( 103 sec) [ -15822.2193] [ 3228] [depth= 1] . ( 113 sec) [ -15820.4640] [ 3226] [depth= 3] . ( 118 sec) [ -15819.5683] [ 3226] [depth= 3] . ( 118 sec) [ -15813.8196] [ 3225] [depth= 3] . ( 118 sec) [ -15811.5725] [ 3224] [depth= 1] . ( 118 sec) [ -15810.3537] [ 3224] [depth= 1] . ( 128 sec) [ -15808.8727] [ 3222] [depth= 2] . ( 130 sec) [ -15807.6121] [ 3221] [depth= 1] . ( 147 sec) [ -15807.5735] [ 3222] [depth= 1] . ( 158 sec) [ -15804.5323] [ 3221] [depth= 1] . ( 165 sec) [ -15801.1029] [ 3221] [depth= 1] . ( 184 sec) [ -15800.4681] [ 3220] [depth= 1] . ( 212 sec) [ -15798.1926] [ 3220] [depth= 1] . ( 213 sec) [ -15797.0965] [ 3220] [depth= 1] . ( 226 sec) [ -15794.7709] [ 3222] [depth= 1] . ( 254 sec) [ -15794.2143] [ 3222] [depth= 1] . ( 254 sec) [ -15794.1026] [ 3222] [depth= 1] . ( 254 sec) [ -15785.1812] [ 3222] [depth= 1] . ( 254 sec) [ -15785.1089] [ 3221] [depth= 1] . ( 283 sec) [ -15784.8354] [ 3221] [depth= 1] . ( 292 sec) [ -15783.8654] [ 3223] [depth= 1] . ( 307 sec) [ -15783.3228] [ 3223] [depth= 1] . ( 307 sec) [ -15783.1490] [ 3219] [depth= 1] . ( 308 sec) [ -15782.9101] [ 3218] [depth= 1] . ( 350 sec) [ -15779.7744] [ 3217] [depth= 1] . ( 350 sec) [ -15778.8310] [ 3217] [depth= 1] . ( 350 sec) [ -15778.0987] [ 3217] [depth= 1] . ( 354 sec) [ -15777.6833] [ 3217] [depth= 1] . ( 366 sec) [ -15777.4593] [ 3218] [depth= 3] . ( 366 sec) [ -15777.3576] [ 3218] [depth= 1] . ( 367 sec) [ -15777.2176] [ 3218] [depth= 1] . ( 373 sec) [ -15776.9660] [ 3220] [depth= 1] . ( 373 sec) [ -15776.3915] [ 3220] [depth= 1] . ( 374 sec) [ -15776.0675] [ 3220] [depth= 1] . ( 379 sec) [ -15774.9012] [ 3220] [depth= 1] . ( 381 sec) [ -15774.4225] [ 3219] [depth= 1] . ( 381 sec) [ -15774.0094] [ 3220] [depth= 1] . ( 383 sec) [ -15773.9069] [ 3220] [depth= 1] . ( 386 sec) [ -15772.6696] [ 3221] [depth= 3] . ( 386 sec) [ -15772.0900] [ 3221] [depth= 1] . ( 387 sec) [ -15771.3463] [ 3220] [depth= 2] . ( 387 sec) [ -15768.7902] [ 3219] [depth= 2] . ( 400 sec) [ -15767.6381] [ 3219] [depth= 1] . ( 413 sec) [ -15766.9461] [ 3219] [depth= 1] . ( 413 sec) [ -15766.6287] [ 3219] [depth= 1] . ( 417 sec) [ -15766.5859] [ 3219] [depth= 1] . ( 420 sec) [ -15766.4429] [ 3219] [depth= 1] . ( 423 sec) [ -15766.1818] [ 3219] [depth= 2] . ( 428 sec) [ -15702.8674] [Branch lengths ] . ( 437 sec) [ -15690.9643] [GTR parameters ] . ( 437 sec) [ -15690.6700] [Alpha ][ 0.520167] . ( 474 sec) [ -15686.5114] [ 3198] [depth= 2] . ( 483 sec) [ -15684.8692] [ 3197] [depth= 1] . ( 524 sec) [ -15681.4742] [ 3200] [depth= 1] . ( 524 sec) [ -15679.9981] [ 3200] [depth= 1] . ( 576 sec) [ -15679.5934] [ 3201] [depth= 1] . ( 628 sec) [ -15679.3542] [ 3200] [depth= 1] . ( 877 sec) [ -15679.0376] [ 3199] [depth= 2] . ( 877 sec) [ -15679.0022] [ 3200] [depth= 1] . ( 892 sec) [ -15678.5062] [ 3199] [depth= 1] . ( 978 sec) [ -15669.4625] [Branch lengths ] . ( 982 sec) [ -15669.4309] [GTR parameters ] . ( 983 sec) [ -15669.2953] [Alpha ][ 0.533139] . ( 1539 sec) [ -15667.1339] [Branch lengths ] . ( 1690 sec) [ -15666.4936] [Branch lengths ] . ( 1690 sec) [ -15666.4936] [Topology ] . ( 1693 sec) [ -15664.4305] [Topology ] . ( 1697 sec) [ -15663.3448] [Topology ] . ( 1700 sec) [ -15662.2873] [Topology ] . ( 1704 sec) [ -15660.2074] [Topology ] . ( 1707 sec) [ -15659.6249] [Topology ] . ( 1711 sec) [ -15659.5561] [Topology ] . ( 1714 sec) [ -15659.5349] [Topology ] . ( 1720 sec) [ -15659.4548] [GTR parameters ] . ( 1721 sec) [ -15659.3474] [Alpha ][ 0.545112] . ( 1721 sec) [ -15659.3474] [Topology ] . ( 1724 sec) [ -15659.3227] [Topology ] . ( 1728 sec) [ -15659.3064] [Topology ] . ( 1731 sec) [ -15659.2947] [Topology ] . ( 1735 sec) [ -15659.2860] [Topology ] . ( 1738 sec) [ -15659.2796] [Topology ] . ( 1742 sec) [ -15659.2748] [Topology ] . ( 1743 sec) [ -15659.2747] [GTR parameters ] . ( 1743 sec) [ -15659.2744] [Alpha ][ 0.545753] . ( 1743 sec) [ -15659.2744] [Topology ] . ( 1746 sec) [ -15659.2706] [Topology ] . ( 1750 sec) [ -15659.2676] [Topology ] . ( 1753 sec) [ -15659.2654] [Topology ] . ( 1757 sec) [ -15659.2637] [Topology ] . ( 1760 sec) [ -15659.2624] [Topology ] . ( 1764 sec) [ -15659.2613] [Topology ] . ( 1765 sec) [ -15659.2610] [GTR parameters ] . ( 1765 sec) [ -15659.2610] [Alpha ][ 0.546299] . ( 1765 sec) [ -15659.2610] [Topology ] . ( 1769 sec) [ -15659.2600] [Topology ] . ( 1770 sec) [ -15659.2600] [GTR parameters ] . ( 1770 sec) [ -15659.2600] [Alpha ][ 0.546299] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15659.260024. . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Time used 0h29m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1753.10user 0.00system 29:57.38elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps