.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2623_139x1044_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... . 959 patterns found. (out of a total of 1044 sites) . 202 sites without polymorphism (19.35%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 71Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 17 sec) [ -48412.0933] [GTR parameters ] . ( 19 sec) [ -47896.6604] [Alpha ][ 0.500960] . ( 20 sec) [ -47896.0418] [11967] [depth= 1] . ( 20 sec) [ -47889.7491] [11967] [depth= 1] . ( 21 sec) [ -47889.7184] [11967] [depth= 1] . ( 23 sec) [ -47884.8015] [11974] [depth= 1] . ( 23 sec) [ -47884.1065] [11967] [depth= 1] . ( 24 sec) [ -47880.9605] [11971] [depth= 1] . ( 26 sec) [ -47879.8054] [11971] [depth= 1] . ( 28 sec) [ -47785.5866] [11978] [depth= 1] . ( 28 sec) [ -47775.6666] [11971] [depth= 1] . ( 30 sec) [ -47721.2414] [11957] [depth= 10] . ( 31 sec) [ -47708.3441] [11936] [depth= 7] . ( 32 sec) [ -47700.5243] [11937] [depth= 1] . ( 33 sec) [ -47653.3192] [11967] [depth= 4] . ( 36 sec) [ -47647.6703] [11962] [depth= 3] . ( 37 sec) [ -47599.1913] [11947] [depth= 8] . ( 37 sec) [ -47535.5539] [11945] [depth= 2] . ( 38 sec) [ -47513.9059] [11901] [depth= 6] . ( 39 sec) [ -47510.9252] [11932] [depth= 1] . ( 40 sec) [ -47508.7762] [11932] [depth= 1] . ( 41 sec) [ -47483.8993] [11896] [depth= 3] . ( 41 sec) [ -47483.2631] [11892] [depth= 2] . ( 42 sec) [ -47426.5354] [11886] [depth= 1] . ( 43 sec) [ -47425.8149] [11884] [depth= 1] . ( 45 sec) [ -47402.6012] [11882] [depth= 1] . ( 47 sec) [ -47395.5346] [11880] [depth= 2] . ( 47 sec) [ -47391.6886] [11880] [depth= 1] . ( 49 sec) [ -47382.4221] [11880] [depth= 1] . ( 50 sec) [ -47381.3623] [11880] [depth= 1] . ( 52 sec) [ -47366.5669] [11880] [depth= 1] . ( 53 sec) [ -47348.4179] [11885] [depth= 1] . ( 54 sec) [ -47341.0681] [11878] [depth= 3] . ( 54 sec) [ -47261.1516] [11837] [depth= 8] . ( 55 sec) [ -47252.1888] [11838] [depth= 1] . ( 56 sec) [ -47249.0172] [11837] [depth= 1] . ( 56 sec) [ -47243.1074] [11829] [depth= 7] . ( 57 sec) [ -47238.7363] [11828] [depth= 2] . ( 58 sec) [ -47217.4023] [11828] [depth= 2] . ( 59 sec) [ -47191.9894] [11815] [depth= 8] . ( 61 sec) [ -47190.7314] [11807] [depth= 1] . ( 61 sec) [ -47189.7649] [11814] [depth= 1] . ( 62 sec) [ -47174.8681] [11812] [depth= 7] . ( 62 sec) [ -47166.6189] [11813] [depth= 2] . ( 65 sec) [ -47160.6317] [11813] [depth= 5] . ( 66 sec) [ -47154.8757] [11806] [depth= 1] . ( 67 sec) [ -47147.9596] [11816] [depth= 2] . ( 68 sec) [ -47109.4212] [11822] [depth= 2] . ( 68 sec) [ -47102.3609] [11821] [depth= 2] . ( 69 sec) [ -47089.8739] [11819] [depth= 1] . ( 69 sec) [ -47089.0613] [11818] [depth= 2] . ( 70 sec) [ -47060.2272] [11822] [depth= 1] . ( 70 sec) [ -47048.6983] [11815] [depth= 9] . ( 71 sec) [ -46998.0362] [11792] [depth= 6] . ( 73 sec) [ -46996.9872] [11797] [depth= 1] . ( 74 sec) [ -46993.5379] [11798] [depth= 1] . ( 76 sec) [ -46975.1927] [11795] [depth= 3] . ( 76 sec) [ -46975.0715] [11795] [depth= 2] . ( 77 sec) [ -46973.8456] [11795] [depth= 1] . ( 77 sec) [ -46967.8534] [11789] [depth= 4] . ( 78 sec) [ -46965.5561] [11793] [depth= 1] . ( 78 sec) [ -46946.5599] [11794] [depth= 1] . ( 79 sec) [ -46944.0629] [11794] [depth= 1] . ( 80 sec) [ -46942.3615] [11791] [depth= 1] . ( 82 sec) [ -46941.8672] [11796] [depth= 1] . ( 84 sec) [ -46940.6928] [11801] [depth= 1] . ( 84 sec) [ -46928.0719] [11796] [depth= 1] . ( 86 sec) [ -46925.2637] [11798] [depth= 1] . ( 87 sec) [ -46923.2189] [11801] [depth= 1] . ( 87 sec) [ -46921.4669] [11798] [depth= 1] . ( 89 sec) [ -46807.1836] [11775] [depth= 9] . ( 90 sec) [ -46803.7842] [11775] [depth= 3] . ( 90 sec) [ -46799.5972] [11770] [depth= 1] . ( 91 sec) [ -46789.9759] [11771] [depth= 2] . ( 92 sec) [ -46789.7951] [11771] [depth= 3] . ( 93 sec) [ -46782.6090] [11766] [depth= 2] . ( 93 sec) [ -46776.4809] [11765] [depth= 1] . ( 95 sec) [ -46748.5989] [11758] [depth= 1] . ( 95 sec) [ -46742.8718] [11756] [depth= 2] . ( 96 sec) [ -46731.3369] [11754] [depth= 2] . ( 97 sec) [ -46708.8195] [11755] [depth= 1] . ( 98 sec) [ -46696.1160] [11762] [depth= 1] . ( 99 sec) [ -46692.1637] [11757] [depth= 1] . ( 99 sec) [ -46690.2295] [11758] [depth= 1] . ( 100 sec) [ -46689.3724] [11760] [depth= 1] . ( 100 sec) [ -46681.0269] [11764] [depth= 1] . ( 101 sec) [ -46675.5669] [11763] [depth= 1] . ( 101 sec) [ -46668.5927] [11762] [depth= 1] . ( 102 sec) [ -46666.2871] [11765] [depth= 1] . ( 103 sec) [ -46664.8495] [11763] [depth= 3] . ( 104 sec) [ -46659.9933] [11762] [depth= 1] . ( 106 sec) [ -46658.0826] [11762] [depth= 1] . ( 106 sec) [ -46656.9028] [11762] [depth= 1] . ( 107 sec) [ -46654.2232] [11763] [depth= 1] . ( 107 sec) [ -46652.4054] [11762] [depth= 1] . ( 108 sec) [ -46627.5128] [11761] [depth= 1] . ( 108 sec) [ -46591.1326] [11755] [depth= 1] . ( 110 sec) [ -46586.4758] [11756] [depth= 1] . ( 111 sec) [ -46585.2054] [11756] [depth= 1] . ( 112 sec) [ -46583.5963] [11757] [depth= 1] . ( 113 sec) [ -46582.9236] [11759] [depth= 1] . ( 113 sec) [ -46578.0240] [11759] [depth= 4] . ( 115 sec) [ -46568.2873] [11766] [depth= 1] . ( 117 sec) [ -46566.7124] [11767] [depth= 1] . ( 118 sec) [ -46562.7181] [11766] [depth= 1] . ( 121 sec) [ -46561.0427] [11765] [depth= 3] . ( 122 sec) [ -46558.4725] [11767] [depth= 1] . ( 122 sec) [ -46557.6097] [11766] [depth= 1] . ( 125 sec) [ -46244.4282] [Branch lengths ] . ( 139 sec) [ -46198.8740] [GTR parameters ] . ( 140 sec) [ -46198.6023] [Alpha ][ 0.490368] . ( 142 sec) [ -46198.2650] [11766] [depth= 1] . ( 142 sec) [ -46198.2387] [11766] [depth= 1] . ( 148 sec) [ -46190.6849] [11767] [depth= 1] . ( 150 sec) [ -46188.7244] [11760] [depth= 2] . ( 151 sec) [ -46177.9868] [11745] [depth= 6] . ( 157 sec) [ -46176.8207] [11779] [depth= 15] . ( 158 sec) [ -46173.3408] [11778] [depth= 3] . ( 161 sec) [ -46172.2590] [11772] [depth= 1] . ( 168 sec) [ -46170.6225] [11771] [depth= 1] . ( 168 sec) [ -46169.2451] [11772] [depth= 2] . ( 170 sec) [ -46167.0315] [11764] [depth= 6] . ( 171 sec) [ -46166.8784] [11764] [depth= 1] . ( 172 sec) [ -46166.4361] [11764] [depth= 2] . ( 173 sec) [ -46166.2089] [11762] [depth= 1] . ( 176 sec) [ -46165.5511] [11761] [depth= 4] . ( 176 sec) [ -46164.6414] [11761] [depth= 1] . ( 177 sec) [ -46162.1245] [11761] [depth= 1] . ( 179 sec) [ -46161.6866] [11761] [depth= 2] . ( 180 sec) [ -46161.6714] [11761] [depth= 1] . ( 181 sec) [ -46159.9442] [11748] [depth= 4] . ( 183 sec) [ -46159.9230] [11747] [depth= 1] . ( 184 sec) [ -46143.8784] [11738] [depth= 8] . ( 188 sec) [ -46143.7093] [11739] [depth= 1] . ( 190 sec) [ -46142.0834] [11737] [depth= 4] . ( 191 sec) [ -46130.1058] [11727] [depth= 2] . ( 202 sec) [ -46125.2536] [11724] [depth= 1] . ( 205 sec) [ -46125.2403] [11724] [depth= 1] . ( 206 sec) [ -46122.1077] [11724] [depth= 2] . ( 207 sec) [ -46121.5802] [11724] [depth= 1] . ( 209 sec) [ -46120.4280] [11724] [depth= 1] . ( 210 sec) [ -46120.3317] [11724] [depth= 1] . ( 212 sec) [ -46117.4096] [11722] [depth= 1] . ( 213 sec) [ -46117.3545] [11719] [depth= 1] . ( 214 sec) [ -46117.3380] [11718] [depth= 1] . ( 215 sec) [ -46115.7129] [11722] [depth= 1] . ( 217 sec) [ -46114.9256] [11724] [depth= 1] . ( 218 sec) [ -46114.2801] [11731] [depth= 1] . ( 221 sec) [ -46113.6489] [11731] [depth= 2] . ( 224 sec) [ -46112.6633] [11731] [depth= 1] . ( 226 sec) [ -46108.7767] [11731] [depth= 1] . ( 229 sec) [ -46107.2229] [11728] [depth= 1] . ( 239 sec) [ -46024.1741] [Branch lengths ] . ( 254 sec) [ -46019.7282] [GTR parameters ] . ( 255 sec) [ -46017.3675] [Alpha ][ 0.519920] . ( 256 sec) [ -46017.0663] [11728] [depth= 1] . ( 266 sec) [ -46007.3656] [11725] [depth= 6] . ( 286 sec) [ -46007.3082] [11725] [depth= 1] . ( 288 sec) [ -46007.2174] [11719] [depth= 2] . ( 297 sec) [ -46006.4687] [11715] [depth= 3] . ( 301 sec) [ -46006.0741] [11716] [depth= 1] . ( 303 sec) [ -46003.3286] [11716] [depth= 1] . ( 319 sec) [ -46003.1201] [11716] [depth= 1] . ( 334 sec) [ -46002.9547] [11717] [depth= 1] . ( 345 sec) [ -45962.1175] [Branch lengths ] . ( 354 sec) [ -45961.2601] [GTR parameters ] . ( 354 sec) [ -45960.4373] [Alpha ][ 0.536211] . ( 356 sec) [ -45960.2402] [11717] [depth= 1] . ( 397 sec) [ -45958.6192] [11719] [depth= 3] . ( 402 sec) [ -45958.1272] [11719] [depth= 2] . ( 442 sec) [ -45936.9832] [Branch lengths ] . ( 457 sec) [ -45936.6276] [GTR parameters ] . ( 457 sec) [ -45936.5482] [Alpha ][ 0.540887] . ( 459 sec) [ -45936.4472] [11719] [depth= 1] . ( 556 sec) [ -45927.5140] [Branch lengths ] . ( 565 sec) [ -45927.2841] [GTR parameters ] . ( 566 sec) [ -45927.2841] [Alpha ][ 0.540887] . ( 568 sec) [ -45927.2447] [11719] [depth= 1] . ( 656 sec) [ -45924.3350] [Branch lengths ] . ( 668 sec) [ -45924.2468] [GTR parameters ] . ( 669 sec) [ -45924.2445] [Alpha ][ 0.539806] . ( 671 sec) [ -45924.2304] [11719] [depth= 1] . ( 768 sec) [ -45923.0869] [Branch lengths ] . ( 776 sec) [ -45923.0542] [GTR parameters ] . ( 777 sec) [ -45923.0514] [Alpha ][ 0.538727] . ( 861 sec) [ -45922.3129] [Branch lengths ] . ( 885 sec) [ -45921.6107] [11726] [depth= 1] . ( 892 sec) [ -45915.6011] [11836] [depth= 8] . ( 908 sec) [ -45914.9599] [11839] [depth= 1] . ( 909 sec) [ -45914.4471] [11856] [depth= 1] . ( 928 sec) [ -45912.1437] [11876] [depth= 6] . ( 974 sec) [ -45908.5078] [11874] [depth= 1] . ( 975 sec) [ -45906.7473] [11883] [depth= 2] . ( 976 sec) [ -45906.7285] [11892] [depth= 2] . ( 983 sec) [ -45905.4768] [11895] [depth= 1] . ( 987 sec) [ -45905.0390] [11897] [depth= 3] . ( 990 sec) [ -45904.5231] [11896] [depth= 5] . ( 1038 sec) [ -45904.1159] [11900] [depth= 3] . ( 1053 sec) [ -45903.2619] [11904] [depth= 1] . ( 1061 sec) [ -45902.0900] [11906] [depth= 1] . ( 1064 sec) [ -45901.8604] [11907] [depth= 1] . ( 1112 sec) [ -45901.4297] [11913] [depth= 1] . ( 1125 sec) [ -45901.1832] [11913] [depth= 1] . ( 1135 sec) [ -45901.1392] [11913] [depth= 1] . ( 1152 sec) [ -45898.9394] [11915] [depth= 1] . ( 1170 sec) [ -45898.8442] [11915] [depth= 1] . ( 1174 sec) [ -45898.2677] [11911] [depth= 1] . ( 1200 sec) [ -45891.7315] [11914] [depth= 2] . ( 1223 sec) [ -45890.2161] [11920] [depth= 1] . ( 1227 sec) [ -45890.1010] [11920] [depth= 1] . ( 1245 sec) [ -45889.7569] [11921] [depth= 1] . ( 1275 sec) [ -45877.3862] [Branch lengths ] . ( 1287 sec) [ -45877.0685] [GTR parameters ] . ( 1288 sec) [ -45876.9248] [Alpha ][ 0.532568] . ( 1295 sec) [ -45875.6979] [11910] [depth= 1] . ( 1301 sec) [ -45875.1151] [11916] [depth= 2] . ( 1319 sec) [ -45871.0555] [11900] [depth= 1] . ( 1387 sec) [ -45870.5407] [11907] [depth= 1] . ( 1419 sec) [ -45870.3767] [11911] [depth= 1] . ( 1473 sec) [ -45870.2067] [11910] [depth= 1] . ( 1554 sec) [ -45869.6311] [11924] [depth= 1] . ( 1729 sec) [ -45863.0817] [Branch lengths ] . ( 1744 sec) [ -45863.0274] [GTR parameters ] . ( 1745 sec) [ -45863.0189] [Alpha ][ 0.531078] . ( 1778 sec) [ -45862.8635] [11898] [depth= 2] . ( 2195 sec) [ -45861.6360] [Branch lengths ] . ( 2203 sec) [ -45861.6305] [GTR parameters ] . ( 2204 sec) [ -45861.6305] [Alpha ][ 0.530547] . ( 2600 sec) [ -45861.4197] [Branch lengths ] . ( 2600 sec) [ -45861.4197] [Topology ] . ( 2609 sec) [ -45861.2722] [Topology ] . ( 2617 sec) [ -45861.0284] [Topology ] . ( 2625 sec) [ -45860.9571] [Topology ] . ( 2633 sec) [ -45860.9148] [Topology ] . ( 2642 sec) [ -45860.8827] [Topology ] . ( 2650 sec) [ -45860.8609] [Topology ] . ( 2658 sec) [ -45860.8453] [Topology ] . ( 2663 sec) [ -45860.8443] [GTR parameters ] . ( 2664 sec) [ -45860.8443] [Alpha ][ 0.530547] . ( 2664 sec) [ -45860.8443] [Topology ] . ( 2672 sec) [ -45860.8330] [Topology ] . ( 2680 sec) [ -45860.8249] [Topology ] . ( 2689 sec) [ -45860.8189] [Topology ] . ( 2697 sec) [ -45860.8146] [Topology ] . ( 2705 sec) [ -45860.8115] [Topology ] . ( 2714 sec) [ -45860.8091] [Topology ] . ( 2716 sec) [ -45860.8091] [GTR parameters ] . ( 2717 sec) [ -45860.8091] [Alpha ][ 0.530547] . ( 2717 sec) [ -45860.8091] [Topology ] . ( 2726 sec) [ -45860.8074] [Topology ] . ( 2735 sec) [ -45860.8062] [Topology ] . ( 2745 sec) [ -45860.8053] [Topology ] . ( 2749 sec) [ -45860.8052] [GTR parameters ] . ( 2750 sec) [ -45860.8052] [Alpha ][ 0.530547] . ( 2750 sec) [ -45860.8052] [Topology ] . ( 2760 sec) [ -45860.8045] [Topology ] . ( 2762 sec) [ -45860.8045] [GTR parameters ] . ( 2762 sec) [ -45860.8045] [Alpha ][ 0.530547] . Checking for NNIs, optimizing five branches... . ( 2856 sec) [ -45860.7494] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2950 sec) [ -45860.7414] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3028 sec) [ -45860.7261] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3108 sec) [ -45860.7249] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -45860.724923. . Printing the most likely tree in file 'nucleic_M2623_139x1044_2006.phy_phyml_tree.txt'... . Time used 0h53m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1890.86user 0.00system 53:18.66elapsed 59%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps