.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2558_27x1060_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 746 patterns found. (out of a total of 1060 sites) . 362 sites without polymorphism (34.15%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 47Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -37472.1429] [Alpha ][ 0.689004] . ( 2 sec) [ -37472.1429] [Topology ] . ( 6 sec) [ -37275.6590] [Topology ] . ( 11 sec) [ -37238.0253] [Topology ] . ( 15 sec) [ -37217.8995] [Topology ] . ( 19 sec) [ -37208.1468] [Topology ] . ( 23 sec) [ -37203.9396] [Topology ] . ( 27 sec) [ -37202.1545] [Topology ] . ( 30 sec) [ -37201.0720] [Topology ] . ( 34 sec) [ -37200.4740] [Topology ] . ( 38 sec) [ -37200.0690] [Topology ] . Checking for NNIs, optimizing five branches... . ( 90 sec) [ -37199.5484] [Topology ] . ( 90 sec) [ -37194.7954] [Alpha ][ 0.615575] . ( 91 sec) [ -37194.7954] [Topology ] . ( 95 sec) [ -37193.2255] [Topology ] . ( 99 sec) [ -37192.6086] [Topology ] . ( 102 sec) [ -37192.3151] [Topology ] . ( 106 sec) [ -37192.1739] [Topology ] . ( 110 sec) [ -37192.1057] [Topology ] . ( 114 sec) [ -37192.0724] [Topology ] . Checking for NNIs, optimizing five branches... . ( 162 sec) [ -37190.4841] [Topology ] . ( 162 sec) [ -37189.3523] [Alpha ][ 0.582519] . ( 163 sec) [ -37189.3523] [Topology ] . ( 167 sec) [ -37188.8012] [Topology ] . ( 171 sec) [ -37188.5915] [Topology ] . ( 174 sec) [ -37188.4981] [Topology ] . ( 178 sec) [ -37188.4556] [Topology ] . ( 182 sec) [ -37188.4359] [Topology ] . ( 186 sec) [ -37188.4268] [Topology ] . Checking for NNIs, optimizing five branches... . ( 232 sec) [ -37188.2745] [Topology ] . ( 233 sec) [ -37187.8143] [Alpha ][ 0.562381] . ( 234 sec) [ -37187.8143] [Topology ] . ( 237 sec) [ -37187.5885] [Topology ] . ( 241 sec) [ -37187.5065] [Topology ] . ( 245 sec) [ -37187.4714] [Topology ] . ( 250 sec) [ -37187.4558] [Topology ] . ( 254 sec) [ -37187.4488] [Topology ] . ( 258 sec) [ -37187.4456] [Topology ] . Checking for NNIs, optimizing five branches... . ( 307 sec) [ -37186.8870] [Topology ] . ( 308 sec) [ -37186.6924] [Alpha ][ 0.549816] . ( 309 sec) [ -37186.6924] [Topology ] . ( 313 sec) [ -37186.5943] [Topology ] . ( 317 sec) [ -37186.5621] [Topology ] . ( 322 sec) [ -37186.5489] [Topology ] . ( 326 sec) [ -37186.5432] [Topology ] . ( 331 sec) [ -37186.5406] [Topology ] . ( 335 sec) [ -37186.5394] [Topology ] . Checking for NNIs, optimizing five branches... . ( 385 sec) [ -37186.4530] [Alpha ][ 0.541753] . ( 385 sec) [ -37186.4530] [Topology ] . ( 390 sec) [ -37186.4112] [Topology ] . ( 394 sec) [ -37186.3977] [Topology ] . ( 398 sec) [ -37186.3922] [Topology ] . ( 403 sec) [ -37186.3898] [Topology ] . ( 408 sec) [ -37186.3887] [Topology ] . ( 412 sec) [ -37186.3881] [Topology ] . Checking for NNIs, optimizing five branches... . ( 459 sec) [ -37186.3475] [Alpha ][ 0.535906] . ( 460 sec) [ -37186.3475] [Topology ] . ( 464 sec) [ -37186.3251] [Topology ] . ( 467 sec) [ -37186.3179] [Topology ] . ( 472 sec) [ -37186.3151] [Topology ] . ( 476 sec) [ -37186.3138] [Topology ] . ( 481 sec) [ -37186.3132] [Topology ] . Checking for NNIs, optimizing five branches... . ( 531 sec) [ -37186.2960] [Alpha ][ 0.532112] . ( 531 sec) [ -37186.2960] [Topology ] . ( 535 sec) [ -37186.2855] [Topology ] . ( 539 sec) [ -37186.2821] [Topology ] . ( 544 sec) [ -37186.2808] [Topology ] . ( 548 sec) [ -37186.2802] [Topology ] . Checking for NNIs, optimizing five branches... . ( 591 sec) [ -37186.2733] [Alpha ][ 0.529697] . ( 591 sec) [ -37186.2733] [Topology ] . ( 595 sec) [ -37186.2682] [Topology ] . ( 599 sec) [ -37186.2664] [Topology ] . ( 602 sec) [ -37186.2657] [Topology ] . Checking for NNIs, optimizing five branches... . ( 645 sec) [ -37186.2628] [Alpha ][ 0.528126] . ( 645 sec) [ -37186.2628] [Topology ] . ( 649 sec) [ -37186.2601] [Topology ] . ( 653 sec) [ -37186.2591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 696 sec) [ -37186.2582] [Alpha ][ 0.527204] . ( 696 sec) [ -37186.2582] [Topology ] . ( 700 sec) [ -37186.2565] [Topology ] . ( 704 sec) [ -37186.2559] [Topology ] . Checking for NNIs, optimizing five branches... . ( 746 sec) [ -37186.2554] [Alpha ][ 0.526493] . ( 746 sec) [ -37186.2554] [Topology ] . ( 750 sec) [ -37186.2544] [Topology ] . ( 754 sec) [ -37186.2540] [Topology ] . Checking for NNIs, optimizing five branches... . ( 796 sec) [ -37186.2537] [Alpha ][ 0.525939] . ( 797 sec) [ -37186.2537] [Topology ] . ( 801 sec) [ -37186.2530] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 885 sec) [ -37472.1429] [Alpha ][ 0.689004] . ( 887 sec) [ -37441.7027] [ 7658] [depth= 1] . ( 888 sec) [ -37425.7851] [ 7666] [depth= 1] . ( 891 sec) [ -37424.7015] [ 7669] [depth= 1] . ( 894 sec) [ -37395.6519] [ 7666] [depth= 1] . ( 896 sec) [ -37395.0472] [ 7667] [depth= 2] . ( 898 sec) [ -37390.6364] [ 7666] [depth= 1] . ( 903 sec) [ -37369.2911] [ 7662] [depth= 2] . ( 904 sec) [ -37358.2377] [ 7651] [depth= 1] . ( 905 sec) [ -37357.1536] [ 7644] [depth= 1] . ( 906 sec) [ -37353.8751] [ 7645] [depth= 1] . ( 909 sec) [ -37350.7777] [ 7648] [depth= 1] . ( 911 sec) [ -37344.0683] [ 7652] [depth= 2] . ( 912 sec) [ -37341.7529] [ 7650] [depth= 1] . ( 913 sec) [ -37340.7846] [ 7645] [depth= 2] . ( 913 sec) [ -37329.8233] [ 7640] [depth= 1] . ( 915 sec) [ -37328.9733] [ 7631] [depth= 1] . ( 917 sec) [ -37324.1842] [ 7636] [depth= 1] . ( 918 sec) [ -37312.8221] [ 7631] [depth= 1] . ( 919 sec) [ -37308.1170] [ 7632] [depth= 1] . ( 920 sec) [ -37303.7814] [ 7638] [depth= 1] . ( 925 sec) [ -37234.4286] [Branch lengths ] . ( 926 sec) [ -37233.5684] [Alpha ][ 0.656739] . ( 937 sec) [ -37230.5585] [ 7641] [depth= 1] . ( 945 sec) [ -37227.8388] [ 7637] [depth= 1] . ( 945 sec) [ -37225.8700] [ 7644] [depth= 1] . ( 947 sec) [ -37221.8936] [ 7644] [depth= 2] . ( 951 sec) [ -37220.5523] [ 7649] [depth= 1] . ( 953 sec) [ -37216.6040] [ 7644] [depth= 1] . ( 959 sec) [ -37215.3248] [ 7645] [depth= 5] . ( 967 sec) [ -37214.2668] [ 7646] [depth= 1] . ( 971 sec) [ -37198.6436] [Branch lengths ] . ( 972 sec) [ -37197.7183] [Alpha ][ 0.624943] . ( 1032 sec) [ -37193.2540] [Branch lengths ] . ( 1032 sec) [ -37193.2540] [Topology ] . ( 1036 sec) [ -37192.4330] [Topology ] . ( 1040 sec) [ -37192.0789] [Topology ] . ( 1044 sec) [ -37191.8886] [Topology ] . ( 1048 sec) [ -37191.7808] [Topology ] . ( 1051 sec) [ -37191.7185] [Topology ] . ( 1055 sec) [ -37191.6814] [Topology ] . ( 1056 sec) [ -37190.1302] [Alpha ][ 0.585852] . ( 1056 sec) [ -37190.1302] [Topology ] . ( 1060 sec) [ -37189.4975] [Topology ] . ( 1064 sec) [ -37189.2439] [Topology ] . ( 1068 sec) [ -37189.1240] [Topology ] . ( 1072 sec) [ -37189.0654] [Topology ] . ( 1076 sec) [ -37189.0356] [Topology ] . ( 1079 sec) [ -37189.0197] [Topology ] . ( 1080 sec) [ -37188.4951] [Alpha ][ 0.564231] . ( 1081 sec) [ -37188.4951] [Topology ] . ( 1084 sec) [ -37188.2354] [Topology ] . ( 1088 sec) [ -37188.1354] [Topology ] . ( 1092 sec) [ -37188.0896] [Topology ] . ( 1096 sec) [ -37188.0677] [Topology ] . ( 1100 sec) [ -37188.0566] [Topology ] . ( 1104 sec) [ -37188.0507] [Topology ] . ( 1104 sec) [ -37187.8241] [Alpha ][ 0.550604] . ( 1105 sec) [ -37187.8241] [Topology ] . ( 1109 sec) [ -37187.7111] [Topology ] . ( 1112 sec) [ -37187.6690] [Topology ] . ( 1116 sec) [ -37187.6501] [Topology ] . ( 1120 sec) [ -37187.6411] [Topology ] . ( 1124 sec) [ -37187.6365] [Topology ] . ( 1128 sec) [ -37187.6340] [Topology ] . ( 1128 sec) [ -37187.5300] [Alpha ][ 0.541711] . ( 1129 sec) [ -37187.5300] [Topology ] . ( 1132 sec) [ -37187.4790] [Topology ] . ( 1136 sec) [ -37187.4603] [Topology ] . ( 1140 sec) [ -37187.4520] [Topology ] . ( 1144 sec) [ -37187.4481] [Topology ] . ( 1148 sec) [ -37187.4460] [Topology ] . ( 1151 sec) [ -37187.4449] [Topology ] . ( 1152 sec) [ -37187.3950] [Alpha ][ 0.535245] . ( 1153 sec) [ -37187.3950] [Topology ] . ( 1156 sec) [ -37187.3675] [Topology ] . ( 1160 sec) [ -37187.3576] [Topology ] . ( 1164 sec) [ -37187.3533] [Topology ] . ( 1168 sec) [ -37187.3512] [Topology ] . ( 1172 sec) [ -37187.3501] [Topology ] . ( 1175 sec) [ -37187.3495] [Topology ] . ( 1176 sec) [ -37187.3269] [Alpha ][ 0.530911] . ( 1176 sec) [ -37187.3269] [Topology ] . ( 1180 sec) [ -37187.3140] [Topology ] . ( 1184 sec) [ -37187.3094] [Topology ] . ( 1188 sec) [ -37187.3073] [Topology ] . ( 1192 sec) [ -37187.3063] [Topology ] . ( 1193 sec) [ -37187.2978] [Alpha ][ 0.528264] . ( 1193 sec) [ -37187.2978] [Topology ] . ( 1197 sec) [ -37187.2913] [Topology ] . ( 1200 sec) [ -37187.2889] [Topology ] . ( 1204 sec) [ -37187.2877] [Topology ] . ( 1208 sec) [ -37187.2872] [Topology ] . ( 1209 sec) [ -37187.2829] [Alpha ][ 0.526362] . ( 1209 sec) [ -37187.2829] [Topology ] . ( 1213 sec) [ -37187.2794] [Topology ] . ( 1217 sec) [ -37187.2781] [Topology ] . ( 1221 sec) [ -37187.2775] [Topology ] . ( 1221 sec) [ -37187.2750] [Alpha ][ 0.524918] . ( 1222 sec) [ -37187.2750] [Topology ] . ( 1225 sec) [ -37187.2729] [Topology ] . ( 1229 sec) [ -37187.2721] [Topology ] . ( 1230 sec) [ -37187.2714] [Alpha ][ 0.524143] . ( 1230 sec) [ -37187.2714] [Topology ] . ( 1234 sec) [ -37187.2702] [Topology ] . ( 1238 sec) [ -37187.2697] [Topology ] . ( 1239 sec) [ -37187.2694] [Alpha ][ 0.523553] . ( 1239 sec) [ -37187.2694] [Topology ] . ( 1243 sec) [ -37187.2687] [Topology ] . ( 1243 sec) [ -37187.2687] [Alpha ][ 0.523553] . Checking for NNIs, optimizing five branches... . ( 1286 sec) [ -37186.8051] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1327 sec) [ -37186.2686] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -37186.253019 . Log likelihood obtained after SPR moves : -37186.268608 . Log likelihood of the current tree: -37186.253019. . Printing the most likely tree in file 'proteic_M2558_27x1060_2005.phy_phyml_tree.txt'... . Time used 0h22m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1316.22user 0.00system 22:48.30elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps