.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2564_142x1130_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... . 780 patterns found. (out of a total of 1130 sites) . 486 sites without polymorphism (43.01%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 8 sec) [ -21575.3354] [GTR parameters ] . ( 9 sec) [ -21206.7214] [Alpha ][ 0.500960] . ( 28 sec) [ -21206.1411] [ 4073] [depth= 1] . ( 40 sec) [ -21204.6228] [ 4081] [depth= 1] . ( 41 sec) [ -21186.6495] [ 4073] [depth= 1] . ( 41 sec) [ -21179.9363] [ 4077] [depth= 1] . ( 42 sec) [ -21168.7735] [ 4065] [depth= 1] . ( 82 sec) [ -21158.8162] [ 4079] [depth= 1] . ( 82 sec) [ -21139.0089] [ 4065] [depth= 1] . ( 88 sec) [ -21135.8801] [ 4078] [depth= 1] . ( 112 sec) [ -21135.5397] [ 4082] [depth= 1] . ( 113 sec) [ -21124.9058] [ 4078] [depth= 1] . ( 137 sec) [ -21118.7827] [ 4078] [depth= 1] . ( 138 sec) [ -21104.9282] [ 4078] [depth= 1] . ( 148 sec) [ -21102.4569] [ 4082] [depth= 1] . ( 148 sec) [ -21093.6963] [ 4078] [depth= 1] . ( 161 sec) [ -21092.7861] [ 4078] [depth= 1] . ( 162 sec) [ -21092.6378] [ 4097] [depth= 4] . ( 169 sec) [ -21068.1089] [ 4085] [depth= 1] . ( 169 sec) [ -21065.4650] [ 4083] [depth= 1] . ( 169 sec) [ -21050.0619] [ 4079] [depth= 1] . ( 171 sec) [ -21049.7466] [ 4092] [depth= 3] . ( 171 sec) [ -21040.6771] [ 4084] [depth= 2] . ( 171 sec) [ -21029.2319] [ 4076] [depth= 2] . ( 172 sec) [ -21027.9744] [ 4065] [depth= 1] . ( 172 sec) [ -21025.1285] [ 4065] [depth= 1] . ( 173 sec) [ -21023.3589] [ 4074] [depth= 3] . ( 173 sec) [ -21021.3107] [ 4079] [depth= 2] . ( 174 sec) [ -21020.1243] [ 4081] [depth= 1] . ( 175 sec) [ -21019.5951] [ 4079] [depth= 1] . ( 221 sec) [ -21017.2476] [ 4078] [depth= 1] . ( 240 sec) [ -21016.7965] [ 4079] [depth= 1] . ( 240 sec) [ -21007.7072] [ 4082] [depth= 1] . ( 246 sec) [ -21004.6349] [ 4081] [depth= 1] . ( 269 sec) [ -20999.8548] [ 4082] [depth= 1] . ( 269 sec) [ -20992.9076] [ 4081] [depth= 1] . ( 289 sec) [ -20991.9812] [ 4082] [depth= 1] . ( 290 sec) [ -20991.1665] [ 4081] [depth= 1] . ( 290 sec) [ -20986.0860] [ 4080] [depth= 1] . ( 291 sec) [ -20980.3861] [ 4081] [depth= 1] . ( 304 sec) [ -20976.1660] [ 4082] [depth= 1] . ( 357 sec) [ -20975.9965] [ 4083] [depth= 1] . ( 358 sec) [ -20975.6405] [ 4082] [depth= 3] . ( 358 sec) [ -20975.0869] [ 4083] [depth= 1] . ( 359 sec) [ -20947.2170] [ 4076] [depth= 4] . ( 359 sec) [ -20944.8007] [ 4076] [depth= 2] . ( 421 sec) [ -20943.7680] [ 4078] [depth= 1] . ( 421 sec) [ -20941.2679] [ 4076] [depth= 1] . ( 422 sec) [ -20940.5185] [ 4076] [depth= 1] . ( 422 sec) [ -20940.2487] [ 4077] [depth= 1] . ( 449 sec) [ -20937.9851] [ 4073] [depth= 12] . ( 491 sec) [ -20929.5728] [ 4072] [depth= 6] . ( 492 sec) [ -20921.3486] [ 4071] [depth= 2] . ( 492 sec) [ -20917.9786] [ 4069] [depth= 7] . ( 499 sec) [ -20916.3278] [ 4069] [depth= 2] . ( 500 sec) [ -20915.3512] [ 4069] [depth= 1] . ( 500 sec) [ -20893.6882] [ 4068] [depth= 2] . ( 501 sec) [ -20888.4796] [ 4062] [depth= 5] . ( 502 sec) [ -20886.3822] [ 4062] [depth= 2] . ( 502 sec) [ -20886.0738] [ 4062] [depth= 1] . ( 503 sec) [ -20885.9162] [ 4062] [depth= 1] . ( 532 sec) [ -20881.2792] [ 4063] [depth= 2] . ( 532 sec) [ -20879.8935] [ 4063] [depth= 1] . ( 546 sec) [ -20878.2185] [ 4068] [depth= 1] . ( 547 sec) [ -20871.1176] [ 4069] [depth= 1] . ( 554 sec) [ -20870.6769] [ 4068] [depth= 1] . ( 563 sec) [ -20869.4644] [ 4068] [depth= 1] . ( 563 sec) [ -20868.7347] [ 4068] [depth= 1] . ( 564 sec) [ -20867.9040] [ 4068] [depth= 1] . ( 564 sec) [ -20860.9312] [ 4067] [depth= 6] . ( 577 sec) [ -20860.8972] [ 4067] [depth= 1] . ( 577 sec) [ -20859.6864] [ 4066] [depth= 1] . ( 668 sec) [ -20857.0629] [ 4066] [depth= 2] . ( 676 sec) [ -20856.8968] [ 4070] [depth= 1] . ( 677 sec) [ -20856.1069] [ 4066] [depth= 1] . ( 705 sec) [ -20854.1021] [ 4067] [depth= 1] . ( 747 sec) [ -20853.7890] [ 4068] [depth= 2] . ( 766 sec) [ -20852.0412] [ 4068] [depth= 2] . ( 773 sec) [ -20851.3324] [ 4068] [depth= 1] . ( 803 sec) [ -20850.3572] [ 4068] [depth= 1] . ( 804 sec) [ -20850.1094] [ 4068] [depth= 1] . ( 839 sec) [ -20850.0652] [ 4068] [depth= 1] . ( 840 sec) [ -20849.3855] [ 4069] [depth= 1] . ( 841 sec) [ -20848.9995] [ 4069] [depth= 1] . ( 868 sec) [ -20848.0215] [ 4069] [depth= 1] . ( 868 sec) [ -20845.6181] [ 4069] [depth= 1] . ( 911 sec) [ -20843.6785] [ 4071] [depth= 1] . ( 911 sec) [ -20836.7597] [ 4069] [depth= 1] . ( 931 sec) [ -20836.7115] [ 4069] [depth= 1] . ( 932 sec) [ -20836.5236] [ 4069] [depth= 1] . ( 932 sec) [ -20836.2225] [ 4069] [depth= 1] . ( 933 sec) [ -20835.6636] [ 4069] [depth= 2] . ( 934 sec) [ -20830.1913] [ 4068] [depth= 1] . ( 934 sec) [ -20825.2374] [ 4067] [depth= 1] . ( 935 sec) [ -20824.8579] [ 4066] [depth= 1] . ( 951 sec) [ -20820.7568] [ 4066] [depth= 1] . ( 968 sec) [ -20819.8356] [ 4067] [depth= 1] . ( 991 sec) [ -20808.0602] [ 4062] [depth= 7] . ( 1002 sec) [ -20802.5850] [ 4062] [depth= 1] . ( 1002 sec) [ -20800.2644] [ 4062] [depth= 1] . ( 1025 sec) [ -20796.7355] [ 4061] [depth= 1] . ( 1025 sec) [ -20792.7739] [ 4061] [depth= 1] . ( 1049 sec) [ -20792.5250] [ 4064] [depth= 1] . ( 1096 sec) [ -20789.3019] [ 4064] [depth= 1] . ( 1097 sec) [ -20786.3729] [ 4063] [depth= 1] . ( 1142 sec) [ -20782.4339] [ 4067] [depth= 4] . ( 1143 sec) [ -20779.6628] [ 4063] [depth= 4] . ( 1143 sec) [ -20767.7524] [ 4060] [depth= 7] . ( 1144 sec) [ -20766.3032] [ 4060] [depth= 1] . ( 1152 sec) [ -20764.9011] [ 4061] [depth= 2] . ( 1152 sec) [ -20762.9082] [ 4060] [depth= 1] . ( 1161 sec) [ -20762.4924] [ 4062] [depth= 8] . ( 1161 sec) [ -20761.6487] [ 4060] [depth= 6] . ( 1188 sec) [ -20758.2501] [ 4059] [depth= 2] . ( 1189 sec) [ -20757.8165] [ 4058] [depth= 1] . ( 1197 sec) [ -20752.8601] [ 4055] [depth= 1] . ( 1258 sec) [ -20752.5236] [ 4058] [depth= 2] . ( 1269 sec) [ -20751.1106] [ 4057] [depth= 3] . ( 1269 sec) [ -20749.8099] [ 4057] [depth= 2] . ( 1272 sec) [ -20737.4337] [ 4052] [depth= 3] . ( 1272 sec) [ -20737.2325] [ 4054] [depth= 2] . ( 1273 sec) [ -20735.3089] [ 4052] [depth= 2] . ( 1273 sec) [ -20735.1284] [ 4053] [depth= 1] . ( 1274 sec) [ -20734.7559] [ 4052] [depth= 1] . ( 1275 sec) [ -20734.6827] [ 4052] [depth= 1] . ( 1290 sec) [ -20733.5590] [ 4052] [depth= 1] . ( 1291 sec) [ -20733.4024] [ 4052] [depth= 1] . ( 1291 sec) [ -20731.3384] [ 4052] [depth= 1] . ( 1292 sec) [ -20730.8938] [ 4052] [depth= 1] . ( 1308 sec) [ -20730.5155] [ 4052] [depth= 1] . ( 1315 sec) [ -20729.2333] [ 4051] [depth= 4] . ( 1315 sec) [ -20729.1189] [ 4051] [depth= 2] . ( 1318 sec) [ -20727.1355] [ 4051] [depth= 1] . ( 1365 sec) [ -20726.9860] [ 4052] [depth= 1] . ( 1372 sec) [ -20724.7169] [ 4052] [depth= 1] . ( 1373 sec) [ -20722.5232] [ 4052] [depth= 2] . ( 1389 sec) [ -20722.2902] [ 4052] [depth= 1] . ( 1397 sec) [ -20721.5908] [ 4052] [depth= 1] . ( 1398 sec) [ -20721.1994] [ 4053] [depth= 1] . ( 1421 sec) [ -20719.3254] [ 4051] [depth= 1] . ( 1423 sec) [ -20570.2004] [Branch lengths ] . ( 1430 sec) [ -20561.4130] [GTR parameters ] . ( 1431 sec) [ -20505.6341] [Alpha ][ 0.340384] . ( 1432 sec) [ -20502.5801] [ 4050] [depth= 1] . ( 1692 sec) [ -20497.9512] [ 4052] [depth= 1] . ( 1727 sec) [ -20497.1532] [ 4056] [depth= 1] . ( 1736 sec) [ -20496.7289] [ 4057] [depth= 4] . ( 1736 sec) [ -20492.9441] [ 4053] [depth= 1] . ( 1764 sec) [ -20491.2348] [ 4057] [depth= 2] . ( 1771 sec) [ -20488.9041] [ 4062] [depth= 1] . ( 1778 sec) [ -20482.4270] [ 4056] [depth= 1] . ( 1779 sec) [ -20476.3787] [ 4050] [depth= 1] . ( 1996 sec) [ -20475.8553] [ 4058] [depth= 1] . ( 2061 sec) [ -20475.7597] [ 4058] [depth= 1] . ( 2298 sec) [ -20475.5956] [ 4059] [depth= 1] . ( 2339 sec) [ -20475.5710] [ 4059] [depth= 1] . ( 2473 sec) [ -20475.5436] [ 4060] [depth= 1] . ( 2474 sec) [ -20475.4362] [ 4059] [depth= 1] . ( 2644 sec) [ -20475.3851] [ 4059] [depth= 1] . ( 2692 sec) [ -20475.3659] [ 4059] [depth= 1] . ( 2815 sec) [ -20472.9853] [ 4058] [depth= 2] . ( 2857 sec) [ -20472.0477] [ 4058] [depth= 1] . ( 2882 sec) [ -20471.9126] [ 4058] [depth= 1] . ( 2894 sec) [ -20465.6123] [ 4055] [depth= 1] . ( 2895 sec) [ -20464.8475] [ 4055] [depth= 1] . ( 3133 sec) [ -20463.6257] [ 4056] [depth= 3] . ( 3194 sec) [ -20462.5867] [ 4057] [depth= 7] . ( 3215 sec) [ -20460.3238] [ 4057] [depth= 1] . ( 3223 sec) [ -20459.9806] [ 4057] [depth= 1] . ( 3223 sec) [ -20458.8099] [ 4057] [depth= 1] . ( 3223 sec) [ -20458.5685] [ 4057] [depth= 1] . ( 3337 sec) [ -20458.2924] [ 4058] [depth= 2] . ( 3386 sec) [ -20457.5555] [ 4060] [depth= 7] . ( 3395 sec) [ -20457.1707] [ 4059] [depth= 1] . ( 3412 sec) [ -20457.1572] [ 4059] [depth= 1] . ( 3425 sec) [ -20457.0323] [ 4059] [depth= 1] . ( 3435 sec) [ -20456.5858] [ 4060] [depth= 1] . ( 3435 sec) [ -20455.9939] [ 4058] [depth= 1] . ( 3508 sec) [ -20455.6505] [ 4062] [depth= 7] . ( 3512 sec) [ -20454.7765] [ 4061] [depth= 1] . ( 3520 sec) [ -20454.2102] [ 4060] [depth= 1] . ( 3538 sec) [ -20422.9616] [Branch lengths ] . ( 3542 sec) [ -20422.0766] [GTR parameters ] . ( 3543 sec) [ -20422.0277] [Alpha ][ 0.336908] . ( 3591 sec) [ -20421.8382] [ 4059] [depth= 1] . ( 3807 sec) [ -20421.6358] [ 4054] [depth= 3] . ( 3808 sec) [ -20421.3499] [ 4052] [depth= 1] . ( 3844 sec) [ -20421.0427] [ 4045] [depth= 1] . ( 4091 sec) [ -20420.8023] [ 4049] [depth= 15] . ( 4144 sec) [ -20420.7856] [ 4049] [depth= 1] . ( 4145 sec) [ -20420.7687] [ 4049] [depth= 1] . ( 4352 sec) [ -20420.7223] [ 4050] [depth= 1] . ( 4468 sec) [ -20420.7116] [ 4050] [depth= 1] . ( 4760 sec) [ -20419.7390] [ 4049] [depth= 1] . ( 5120 sec) [ -20419.5222] [ 4049] [depth= 1] . ( 5305 sec) [ -20413.7382] [Branch lengths ] . ( 5310 sec) [ -20413.6360] [GTR parameters ] . ( 5311 sec) [ -20413.6033] [Alpha ][ 0.339837] . ( 5593 sec) [ -20413.3475] [ 4053] [depth= 3] . ( 5904 sec) [ -20413.2895] [ 4055] [depth= 2] . ( 5976 sec) [ -20412.2258] [ 4053] [depth= 3] . ( 6012 sec) [ -20411.1385] [ 4055] [depth= 1] . ( 6012 sec) [ -20411.1155] [ 4056] [depth= 1] . ( 6013 sec) [ -20410.5727] [ 4056] [depth= 1] . ( 6144 sec) [ -20410.5137] [ 4055] [depth= 1] . ( 7016 sec) [ -20409.1116] [Branch lengths ] . ( 7020 sec) [ -20409.0854] [GTR parameters ] . ( 7020 sec) [ -20409.0850] [Alpha ][ 0.339416] . ( 7376 sec) [ -20408.9236] [ 4056] [depth= 1] . ( 8419 sec) [ -20408.0906] [Branch lengths ] . ( 8421 sec) [ -20408.0875] [GTR parameters ] . ( 8421 sec) [ -20408.0864] [Alpha ][ 0.339917] . ( 8628 sec) [ -20408.0615] [ 4055] [depth= 1] . ( 8672 sec) [ -20406.7339] [Branch lengths ] . ( 8673 sec) [ -20406.7326] [GTR parameters ] . ( 8673 sec) [ -20406.7326] [Alpha ][ 0.339917] . ( 8925 sec) [ -20404.3740] [Branch lengths ] . ( 8926 sec) [ -20404.3740] [Topology ] . ( 8931 sec) [ -20401.7657] [Topology ] . ( 8936 sec) [ -20398.2826] [Topology ] . ( 8941 sec) [ -20397.4685] [Topology ] . ( 8946 sec) [ -20397.3083] [Topology ] . ( 8951 sec) [ -20397.2770] [Topology ] . ( 8956 sec) [ -20397.2704] [Topology ] . ( 8961 sec) [ -20397.2689] [Topology ] . ( 8965 sec) [ -20397.2675] [GTR parameters ] . ( 8965 sec) [ -20397.2667] [Alpha ][ 0.340321] . ( 8965 sec) [ -20397.2667] [Topology ] . ( 8970 sec) [ -20397.2662] [Topology ] . ( 8971 sec) [ -20397.2662] [GTR parameters ] . ( 8972 sec) [ -20397.2662] [Alpha ][ 0.340321] . Checking for NNIs, optimizing five branches... . ( 9008 sec) [ -20397.2588] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20397.258808. . Printing the most likely tree in file 'nucleic_M2564_142x1130_2006.phy_phyml_tree.txt'... . Time used 2h30m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 6839.56user 0.00system 2:30:46elapsed 75%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps