.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2587_117x1910_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... . 1192 patterns found. (out of a total of 1910 sites) . 932 sites without polymorphism (48.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 74Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -17118.5858] [GTR parameters ] . ( 8 sec) [ -17061.9139] [Alpha ][ 0.510962] . ( 11 sec) [ -17061.8486] [ 2501] [depth= 1] . ( 12 sec) [ -17061.5245] [ 2503] [depth= 1] . ( 14 sec) [ -17061.3940] [ 2503] [depth= 1] . ( 15 sec) [ -17055.7601] [ 2503] [depth= 1] . ( 16 sec) [ -17054.4582] [ 2504] [depth= 1] . ( 16 sec) [ -17048.2848] [ 2503] [depth= 1] . ( 17 sec) [ -17048.1573] [ 2503] [depth= 1] . ( 17 sec) [ -17012.1744] [ 2499] [depth= 2] . ( 18 sec) [ -17011.1295] [ 2500] [depth= 1] . ( 19 sec) [ -17008.9932] [ 2499] [depth= 1] . ( 20 sec) [ -17007.7526] [ 2498] [depth= 2] . ( 22 sec) [ -16997.0382] [ 2497] [depth= 1] . ( 24 sec) [ -16988.9504] [ 2496] [depth= 1] . ( 24 sec) [ -16986.8155] [ 2494] [depth= 1] . ( 25 sec) [ -16986.6340] [ 2495] [depth= 1] . ( 26 sec) [ -16984.9873] [ 2498] [depth= 1] . ( 26 sec) [ -16981.1079] [ 2498] [depth= 1] . ( 27 sec) [ -16978.1535] [ 2498] [depth= 3] . ( 27 sec) [ -16977.9780] [ 2499] [depth= 1] . ( 28 sec) [ -16975.2247] [ 2498] [depth= 1] . ( 28 sec) [ -16969.3938] [ 2497] [depth= 1] . ( 29 sec) [ -16968.6801] [ 2499] [depth= 1] . ( 29 sec) [ -16941.9979] [ 2490] [depth= 3] . ( 30 sec) [ -16940.4873] [ 2489] [depth= 1] . ( 30 sec) [ -16939.8321] [ 2488] [depth= 2] . ( 31 sec) [ -16939.6579] [ 2488] [depth= 1] . ( 32 sec) [ -16938.7979] [ 2490] [depth= 3] . ( 33 sec) [ -16938.4292] [ 2491] [depth= 1] . ( 33 sec) [ -16938.3078] [ 2490] [depth= 2] . ( 33 sec) [ -16937.3245] [ 2490] [depth= 1] . ( 34 sec) [ -16937.0116] [ 2490] [depth= 1] . ( 35 sec) [ -16936.7720] [ 2490] [depth= 1] . ( 36 sec) [ -16929.7948] [ 2492] [depth= 1] . ( 36 sec) [ -16924.2174] [ 2491] [depth= 2] . ( 38 sec) [ -16911.7561] [ 2488] [depth= 1] . ( 39 sec) [ -16907.5293] [ 2488] [depth= 1] . ( 40 sec) [ -16905.3548] [ 2488] [depth= 1] . ( 40 sec) [ -16877.3714] [ 2486] [depth= 2] . ( 41 sec) [ -16848.2452] [ 2479] [depth= 2] . ( 44 sec) [ -16847.5262] [ 2480] [depth= 2] . ( 45 sec) [ -16845.7151] [ 2478] [depth= 1] . ( 45 sec) [ -16833.2815] [ 2479] [depth= 5] . ( 46 sec) [ -16815.1570] [ 2477] [depth= 5] . ( 49 sec) [ -16814.0064] [ 2477] [depth= 1] . ( 50 sec) [ -16807.4038] [ 2478] [depth= 6] . ( 51 sec) [ -16804.1323] [ 2478] [depth= 2] . ( 51 sec) [ -16802.1090] [ 2478] [depth= 4] . ( 51 sec) [ -16793.5405] [ 2478] [depth= 1] . ( 52 sec) [ -16768.5916] [ 2483] [depth= 3] . ( 52 sec) [ -16720.6904] [ 2468] [depth= 3] . ( 52 sec) [ -16710.6190] [ 2468] [depth= 4] . ( 53 sec) [ -16664.5551] [ 2460] [depth= 10] . ( 53 sec) [ -16656.6646] [ 2460] [depth= 1] . ( 53 sec) [ -16653.7134] [ 2459] [depth= 1] . ( 54 sec) [ -16634.4284] [ 2458] [depth= 2] . ( 54 sec) [ -16633.8186] [ 2457] [depth= 1] . ( 54 sec) [ -16629.0993] [ 2457] [depth= 1] . ( 55 sec) [ -16612.3678] [ 2454] [depth= 1] . ( 55 sec) [ -16588.9138] [ 2453] [depth= 1] . ( 55 sec) [ -16587.1099] [ 2453] [depth= 1] . ( 56 sec) [ -16585.3977] [ 2451] [depth= 1] . ( 56 sec) [ -16570.3859] [ 2450] [depth= 2] . ( 56 sec) [ -16558.7194] [ 2447] [depth= 2] . ( 57 sec) [ -16551.4450] [ 2447] [depth= 1] . ( 59 sec) [ -16550.6123] [ 2448] [depth= 1] . ( 60 sec) [ -16537.2948] [ 2447] [depth= 1] . ( 60 sec) [ -16537.1023] [ 2447] [depth= 1] . ( 63 sec) [ -16536.6356] [ 2448] [depth= 5] . ( 63 sec) [ -16536.5111] [ 2445] [depth= 6] . ( 64 sec) [ -16533.1132] [ 2445] [depth= 1] . ( 64 sec) [ -16530.7956] [ 2446] [depth= 1] . ( 65 sec) [ -16527.7890] [ 2446] [depth= 1] . ( 65 sec) [ -16518.3524] [ 2444] [depth= 1] . ( 66 sec) [ -16477.2808] [ 2443] [depth= 2] . ( 66 sec) [ -16475.6929] [ 2442] [depth= 2] . ( 66 sec) [ -16444.7209] [ 2438] [depth= 3] . ( 67 sec) [ -16433.8394] [ 2438] [depth= 2] . ( 68 sec) [ -16420.0941] [ 2436] [depth= 1] . ( 68 sec) [ -16414.7122] [ 2435] [depth= 1] . ( 69 sec) [ -16414.4033] [ 2436] [depth= 1] . ( 70 sec) [ -16412.3239] [ 2435] [depth= 1] . ( 70 sec) [ -16411.8317] [ 2440] [depth= 2] . ( 73 sec) [ -16411.6088] [ 2440] [depth= 1] . ( 73 sec) [ -16386.9789] [ 2432] [depth= 11] . ( 74 sec) [ -16375.2206] [ 2430] [depth= 1] . ( 74 sec) [ -16340.5658] [ 2420] [depth= 11] . ( 74 sec) [ -16337.9436] [ 2423] [depth= 1] . ( 75 sec) [ -16336.0694] [ 2420] [depth= 1] . ( 75 sec) [ -16332.6989] [ 2420] [depth= 2] . ( 76 sec) [ -16317.8764] [ 2417] [depth= 1] . ( 76 sec) [ -16315.7141] [ 2420] [depth= 1] . ( 77 sec) [ -16311.1329] [ 2420] [depth= 1] . ( 78 sec) [ -16308.4740] [ 2419] [depth= 5] . ( 78 sec) [ -16302.2313] [ 2415] [depth= 2] . ( 83 sec) [ -16300.8847] [ 2414] [depth= 1] . ( 88 sec) [ -16300.3938] [ 2414] [depth= 5] . ( 89 sec) [ -16299.8693] [ 2415] [depth= 1] . ( 91 sec) [ -16299.8225] [ 2415] [depth= 1] . ( 91 sec) [ -16299.5804] [ 2415] [depth= 1] . ( 91 sec) [ -16299.5675] [ 2415] [depth= 1] . ( 93 sec) [ -16299.1221] [ 2415] [depth= 1] . ( 95 sec) [ -16299.1110] [ 2415] [depth= 1] . ( 96 sec) [ -16298.9413] [ 2415] [depth= 1] . ( 98 sec) [ -16298.7875] [ 2415] [depth= 1] . ( 108 sec) [ -16298.4173] [ 2414] [depth= 2] . ( 108 sec) [ -16297.4455] [ 2415] [depth= 3] . ( 111 sec) [ -16295.6015] [ 2414] [depth= 1] . ( 113 sec) [ -16293.9554] [ 2415] [depth= 1] . ( 114 sec) [ -16293.8110] [ 2413] [depth= 3] . ( 114 sec) [ -16293.3504] [ 2413] [depth= 1] . ( 114 sec) [ -16293.1993] [ 2413] [depth= 1] . ( 115 sec) [ -16292.1502] [ 2413] [depth= 2] . ( 116 sec) [ -16291.6914] [ 2411] [depth= 1] . ( 116 sec) [ -16291.4998] [ 2411] [depth= 3] . ( 116 sec) [ -16286.5956] [ 2410] [depth= 1] . ( 117 sec) [ -16285.2249] [ 2410] [depth= 1] . ( 118 sec) [ -16284.7493] [ 2411] [depth= 1] . ( 118 sec) [ -16284.2564] [ 2411] [depth= 8] . ( 121 sec) [ -16283.9869] [ 2411] [depth= 1] . ( 121 sec) [ -16283.6030] [ 2411] [depth= 3] . ( 121 sec) [ -16283.5534] [ 2411] [depth= 2] . ( 125 sec) [ -16282.9945] [ 2413] [depth= 1] . ( 128 sec) [ -16282.7010] [ 2413] [depth= 1] . ( 128 sec) [ -16282.5971] [ 2412] [depth= 2] . ( 128 sec) [ -16282.0522] [ 2412] [depth= 1] . ( 129 sec) [ -16281.8022] [ 2412] [depth= 1] . ( 130 sec) [ -16281.7418] [ 2412] [depth= 2] . ( 131 sec) [ -16281.4656] [ 2413] [depth= 1] . ( 139 sec) [ -16281.3579] [ 2413] [depth= 1] . ( 141 sec) [ -16120.0277] [Branch lengths ] . ( 147 sec) [ -16117.5178] [GTR parameters ] . ( 148 sec) [ -16117.3171] [Alpha ][ 0.528134] . ( 151 sec) [ -16116.7830] [ 2412] [depth= 1] . ( 156 sec) [ -16116.6175] [ 2411] [depth= 1] . ( 165 sec) [ -16116.5757] [ 2408] [depth= 1] . ( 168 sec) [ -16115.5897] [ 2411] [depth= 1] . ( 169 sec) [ -16115.4180] [ 2411] [depth= 2] . ( 174 sec) [ -16115.1206] [ 2411] [depth= 1] . ( 174 sec) [ -16114.8013] [ 2410] [depth= 2] . ( 175 sec) [ -16114.6590] [ 2410] [depth= 1] . ( 175 sec) [ -16114.6324] [ 2412] [depth= 2] . ( 176 sec) [ -16113.4557] [ 2413] [depth= 1] . ( 186 sec) [ -16113.1497] [ 2413] [depth= 1] . ( 190 sec) [ -16112.8715] [ 2414] [depth= 1] . ( 201 sec) [ -16112.7857] [ 2414] [depth= 1] . ( 203 sec) [ -16112.6531] [ 2414] [depth= 1] . ( 212 sec) [ -16112.5534] [ 2414] [depth= 1] . ( 212 sec) [ -16110.8717] [ 2413] [depth= 9] . ( 215 sec) [ -16100.3139] [ 2414] [depth= 13] . ( 223 sec) [ -16097.6759] [ 2412] [depth= 1] . ( 227 sec) [ -16095.1643] [ 2409] [depth= 1] . ( 246 sec) [ -16093.4681] [ 2408] [depth= 2] . ( 257 sec) [ -16093.4250] [ 2408] [depth= 1] . ( 260 sec) [ -16093.3742] [ 2408] [depth= 1] . ( 274 sec) [ -16093.0488] [ 2408] [depth= 1] . ( 275 sec) [ -16092.8752] [ 2407] [depth= 1] . ( 284 sec) [ -16091.5530] [ 2407] [depth= 5] . ( 284 sec) [ -16091.5119] [ 2407] [depth= 2] . ( 292 sec) [ -16091.4425] [ 2406] [depth= 1] . ( 293 sec) [ -16091.0760] [ 2406] [depth= 1] . ( 300 sec) [ -16091.0628] [ 2406] [depth= 2] . ( 310 sec) [ -16091.0346] [ 2406] [depth= 3] . ( 312 sec) [ -16090.8085] [ 2406] [depth= 1] . ( 314 sec) [ -16090.6981] [ 2406] [depth= 1] . ( 317 sec) [ -16090.2993] [ 2406] [depth= 2] . ( 319 sec) [ -16090.2692] [ 2406] [depth= 2] . ( 327 sec) [ -16090.2045] [ 2406] [depth= 2] . ( 330 sec) [ -16090.1847] [ 2406] [depth= 1] . ( 333 sec) [ -16040.0961] [Branch lengths ] . ( 337 sec) [ -16039.9837] [GTR parameters ] . ( 338 sec) [ -16036.8921] [Alpha ][ 0.467227] . ( 340 sec) [ -16036.7681] [ 2407] [depth= 1] . ( 357 sec) [ -16031.8905] [ 2404] [depth= 1] . ( 357 sec) [ -16031.4071] [ 2403] [depth= 2] . ( 358 sec) [ -16031.3782] [ 2403] [depth= 1] . ( 363 sec) [ -16031.1151] [ 2403] [depth= 2] . ( 363 sec) [ -16031.0280] [ 2403] [depth= 1] . ( 364 sec) [ -16031.0166] [ 2403] [depth= 2] . ( 365 sec) [ -16031.0056] [ 2403] [depth= 1] . ( 367 sec) [ -16030.2336] [ 2403] [depth= 3] . ( 368 sec) [ -16029.6962] [ 2400] [depth= 1] . ( 369 sec) [ -16029.4872] [ 2405] [depth= 2] . ( 390 sec) [ -16029.4538] [ 2405] [depth= 1] . ( 395 sec) [ -16029.2589] [ 2407] [depth= 1] . ( 395 sec) [ -16029.1713] [ 2407] [depth= 1] . ( 402 sec) [ -16029.0985] [ 2407] [depth= 1] . ( 414 sec) [ -16028.8793] [ 2407] [depth= 1] . ( 419 sec) [ -16028.8346] [ 2407] [depth= 1] . ( 446 sec) [ -16028.8198] [ 2407] [depth= 2] . ( 450 sec) [ -16028.8032] [ 2407] [depth= 1] . ( 460 sec) [ -16028.7826] [ 2408] [depth= 1] . ( 460 sec) [ -16028.5403] [ 2408] [depth= 1] . ( 461 sec) [ -16027.8104] [ 2408] [depth= 3] . ( 464 sec) [ -16027.6439] [ 2408] [depth= 2] . ( 469 sec) [ -16027.6317] [ 2408] [depth= 1] . ( 479 sec) [ -16027.6212] [ 2408] [depth= 2] . ( 496 sec) [ -16027.4481] [ 2408] [depth= 1] . ( 497 sec) [ -16027.2664] [ 2408] [depth= 3] . ( 503 sec) [ -16027.2541] [ 2408] [depth= 2] . ( 504 sec) [ -16027.2126] [ 2408] [depth= 1] . ( 508 sec) [ -16002.9456] [Branch lengths ] . ( 513 sec) [ -16002.7906] [GTR parameters ] . ( 513 sec) [ -16000.4331] [Alpha ][ 0.422057] . ( 516 sec) [ -16000.3959] [ 2407] [depth= 1] . ( 537 sec) [ -16000.3540] [ 2407] [depth= 1] . ( 539 sec) [ -16000.3002] [ 2407] [depth= 3] . ( 540 sec) [ -16000.0417] [ 2408] [depth= 1] . ( 627 sec) [ -16000.0259] [ 2408] [depth= 2] . ( 629 sec) [ -16000.0130] [ 2408] [depth= 1] . ( 641 sec) [ -15999.9830] [ 2408] [depth= 1] . ( 642 sec) [ -15999.8588] [ 2408] [depth= 1] . ( 649 sec) [ -15999.8418] [ 2408] [depth= 2] . ( 650 sec) [ -15999.8207] [ 2408] [depth= 3] . ( 663 sec) [ -15999.7982] [ 2409] [depth= 2] . ( 664 sec) [ -15999.7368] [ 2408] [depth= 2] . ( 674 sec) [ -15999.6409] [ 2408] [depth= 2] . ( 681 sec) [ -15999.6013] [ 2408] [depth= 2] . ( 687 sec) [ -15999.5604] [ 2408] [depth= 1] . ( 693 sec) [ -15989.0826] [Branch lengths ] . ( 698 sec) [ -15989.0499] [GTR parameters ] . ( 698 sec) [ -15987.9969] [Alpha ][ 0.395290] . ( 720 sec) [ -15987.9328] [ 2408] [depth= 2] . ( 720 sec) [ -15987.8818] [ 2408] [depth= 1] . ( 725 sec) [ -15987.8153] [ 2408] [depth= 2] . ( 726 sec) [ -15987.5197] [ 2407] [depth= 2] . ( 853 sec) [ -15987.4816] [ 2407] [depth= 2] . ( 870 sec) [ -15987.4657] [ 2408] [depth= 6] . ( 912 sec) [ -15981.5061] [Branch lengths ] . ( 917 sec) [ -15981.4902] [GTR parameters ] . ( 917 sec) [ -15980.8927] [Alpha ][ 0.376640] . ( 938 sec) [ -15980.8238] [ 2408] [depth= 1] . ( 944 sec) [ -15980.7971] [ 2408] [depth= 3] . ( 1001 sec) [ -15980.7581] [ 2409] [depth= 1] . ( 1058 sec) [ -15980.7039] [ 2409] [depth= 3] . ( 1067 sec) [ -15980.6883] [ 2409] [depth= 2] . ( 1108 sec) [ -15980.6701] [ 2409] [depth= 2] . ( 1129 sec) [ -15977.3202] [Branch lengths ] . ( 1131 sec) [ -15977.3140] [GTR parameters ] . ( 1132 sec) [ -15977.0609] [Alpha ][ 0.365243] . ( 1157 sec) [ -15977.0475] [ 2409] [depth= 3] . ( 1341 sec) [ -15975.2870] [Branch lengths ] . ( 1344 sec) [ -15975.2842] [GTR parameters ] . ( 1345 sec) [ -15975.1797] [Alpha ][ 0.358283] . ( 1565 sec) [ -15972.6765] [Branch lengths ] . ( 1582 sec) [ -15972.5604] [ 2408] [depth= 1] . ( 1653 sec) [ -15972.3747] [ 2407] [depth= 1] . ( 1845 sec) [ -15972.0369] [ 2407] [depth= 4] . ( 1856 sec) [ -15972.0154] [ 2407] [depth= 1] . ( 1897 sec) [ -15970.2284] [Branch lengths ] . ( 1901 sec) [ -15970.2234] [GTR parameters ] . ( 1902 sec) [ -15970.0689] [Alpha ][ 0.350001] . ( 2158 sec) [ -15970.0552] [ 2407] [depth= 1] . ( 2203 sec) [ -15969.8029] [Branch lengths ] . ( 2207 sec) [ -15969.8020] [GTR parameters ] . ( 2208 sec) [ -15969.7841] [Alpha ][ 0.347103] . ( 2208 sec) [ -15969.7841] [Topology ] . ( 2215 sec) [ -15969.7074] [Topology ] . ( 2221 sec) [ -15969.6648] [Topology ] . ( 2228 sec) [ -15969.6366] [Topology ] . ( 2234 sec) [ -15969.6176] [Topology ] . ( 2241 sec) [ -15969.6046] [Topology ] . ( 2247 sec) [ -15969.5957] [Topology ] . ( 2249 sec) [ -15969.5950] [GTR parameters ] . ( 2250 sec) [ -15969.5740] [Alpha ][ 0.344014] . ( 2250 sec) [ -15969.5740] [Topology ] . ( 2256 sec) [ -15969.5590] [Topology ] . ( 2263 sec) [ -15969.5490] [Topology ] . ( 2269 sec) [ -15969.5422] [Topology ] . ( 2276 sec) [ -15969.5374] [Topology ] . ( 2283 sec) [ -15969.5341] [Topology ] . ( 2289 sec) [ -15969.5318] [Topology ] . ( 2292 sec) [ -15969.5314] [GTR parameters ] . ( 2292 sec) [ -15969.5264] [Alpha ][ 0.342506] . ( 2292 sec) [ -15969.5264] [Topology ] . ( 2299 sec) [ -15969.5226] [Topology ] . ( 2306 sec) [ -15969.5200] [Topology ] . ( 2312 sec) [ -15969.5182] [Topology ] . ( 2319 sec) [ -15969.5169] [Topology ] . ( 2325 sec) [ -15969.5160] [Topology ] . ( 2326 sec) [ -15969.5159] [GTR parameters ] . ( 2327 sec) [ -15969.5150] [Alpha ][ 0.341829] . ( 2327 sec) [ -15969.5150] [Topology ] . ( 2334 sec) [ -15969.5138] [Topology ] . ( 2340 sec) [ -15969.5129] [Topology ] . ( 2341 sec) [ -15969.5129] [GTR parameters ] . ( 2342 sec) [ -15969.5129] [Alpha ][ 0.341487] . ( 2342 sec) [ -15969.5129] [Topology ] . ( 2349 sec) [ -15969.5121] [Topology ] . ( 2350 sec) [ -15969.5121] [GTR parameters ] . ( 2350 sec) [ -15969.5121] [Alpha ][ 0.341487] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15969.512094. . Printing the most likely tree in file 'nucleic_M2587_117x1910_2006.phy_phyml_tree.txt'... . Time used 0h39m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2380.93user 0.00system 40:02.08elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps