.......................... 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)... . ( 10 sec) [ -17118.5858] [GTR parameters ] . ( 11 sec) [ -17061.9139] [Alpha ][ 0.510962] . ( 138 sec) [ -17061.8486] [ 2501] [depth= 1] . ( 148 sec) [ -17061.5245] [ 2503] [depth= 1] . ( 212 sec) [ -17061.3940] [ 2503] [depth= 1] . ( 212 sec) [ -17055.7601] [ 2503] [depth= 1] . ( 229 sec) [ -17054.4582] [ 2504] [depth= 1] . ( 230 sec) [ -17048.2848] [ 2503] [depth= 1] . ( 239 sec) [ -17048.1573] [ 2503] [depth= 1] . ( 239 sec) [ -17012.1744] [ 2499] [depth= 2] . ( 241 sec) [ -17011.1295] [ 2500] [depth= 1] . ( 260 sec) [ -17008.9932] [ 2499] [depth= 1] . ( 287 sec) [ -17007.7526] [ 2498] [depth= 2] . ( 313 sec) [ -16997.0382] [ 2497] [depth= 1] . ( 347 sec) [ -16988.9504] [ 2496] [depth= 1] . ( 356 sec) [ -16986.8155] [ 2494] [depth= 1] . ( 381 sec) [ -16986.6340] [ 2495] [depth= 1] . ( 390 sec) [ -16984.9873] [ 2498] [depth= 1] . ( 391 sec) [ -16981.1079] [ 2498] [depth= 1] . ( 392 sec) [ -16978.1535] [ 2498] [depth= 3] . ( 392 sec) [ -16977.9780] [ 2499] [depth= 1] . ( 393 sec) [ -16975.2247] [ 2498] [depth= 1] . ( 412 sec) [ -16969.3938] [ 2497] [depth= 1] . ( 420 sec) [ -16968.6801] [ 2499] [depth= 1] . ( 421 sec) [ -16941.9979] [ 2490] [depth= 3] . ( 431 sec) [ -16940.4873] [ 2489] [depth= 1] . ( 432 sec) [ -16939.8321] [ 2488] [depth= 2] . ( 432 sec) [ -16939.6579] [ 2488] [depth= 1] . ( 436 sec) [ -16938.7979] [ 2490] [depth= 3] . ( 437 sec) [ -16938.4292] [ 2491] [depth= 1] . ( 439 sec) [ -16938.3078] [ 2490] [depth= 2] . ( 439 sec) [ -16937.3245] [ 2490] [depth= 1] . ( 440 sec) [ -16937.0116] [ 2490] [depth= 1] . ( 466 sec) [ -16936.7720] [ 2490] [depth= 1] . ( 490 sec) [ -16929.7948] [ 2492] [depth= 1] . ( 491 sec) [ -16924.2174] [ 2491] [depth= 2] . ( 515 sec) [ -16911.7561] [ 2488] [depth= 1] . ( 549 sec) [ -16901.3628] [ 2504] [depth= 4] . ( 549 sec) [ -16869.1525] [ 2497] [depth= 4] . ( 550 sec) [ -16864.7730] [ 2497] [depth= 1] . ( 550 sec) [ -16862.4465] [ 2497] [depth= 1] . ( 551 sec) [ -16850.8247] [ 2491] [depth= 3] . ( 552 sec) [ -16822.4027] [ 2485] [depth= 3] . ( 625 sec) [ -16821.4911] [ 2486] [depth= 2] . ( 626 sec) [ -16819.9243] [ 2484] [depth= 1] . ( 627 sec) [ -16806.5495] [ 2484] [depth= 5] . ( 627 sec) [ -16788.2124] [ 2482] [depth= 5] . ( 674 sec) [ -16787.1030] [ 2482] [depth= 1] . ( 685 sec) [ -16780.1704] [ 2483] [depth= 6] . ( 686 sec) [ -16774.4987] [ 2485] [depth= 1] . ( 686 sec) [ -16767.6995] [ 2483] [depth= 1] . ( 697 sec) [ -16746.8228] [ 2484] [depth= 3] . ( 698 sec) [ -16710.9466] [ 2475] [depth= 4] . ( 698 sec) [ -16710.6731] [ 2475] [depth= 9] . ( 699 sec) [ -16664.1930] [ 2461] [depth= 5] . ( 700 sec) [ -16653.3183] [ 2463] [depth= 3] . ( 701 sec) [ -16650.4056] [ 2463] [depth= 1] . ( 701 sec) [ -16640.5292] [ 2466] [depth= 2] . ( 702 sec) [ -16623.3821] [ 2459] [depth= 3] . ( 702 sec) [ -16622.3660] [ 2460] [depth= 1] . ( 703 sec) [ -16612.8832] [ 2464] [depth= 6] . ( 705 sec) [ -16605.4180] [ 2463] [depth= 3] . ( 705 sec) [ -16588.9581] [ 2463] [depth= 1] . ( 706 sec) [ -16588.4739] [ 2463] [depth= 1] . ( 707 sec) [ -16584.1319] [ 2461] [depth= 1] . ( 715 sec) [ -16564.9228] [ 2458] [depth= 4] . ( 716 sec) [ -16562.2050] [ 2456] [depth= 1] . ( 724 sec) [ -16557.0012] [ 2451] [depth= 10] . ( 734 sec) [ -16556.3796] [ 2451] [depth= 1] . ( 744 sec) [ -16553.1539] [ 2451] [depth= 1] . ( 745 sec) [ -16551.9151] [ 2449] [depth= 4] . ( 745 sec) [ -16550.3976] [ 2448] [depth= 4] . ( 746 sec) [ -16547.8495] [ 2448] [depth= 2] . ( 755 sec) [ -16547.3379] [ 2448] [depth= 2] . ( 756 sec) [ -16541.8320] [ 2448] [depth= 1] . ( 756 sec) [ -16535.5575] [ 2447] [depth= 1] . ( 757 sec) [ -16535.4042] [ 2447] [depth= 1] . ( 768 sec) [ -16522.6571] [ 2454] [depth= 3] . ( 769 sec) [ -16496.0961] [ 2446] [depth= 3] . ( 770 sec) [ -16496.0498] [ 2447] [depth= 1] . ( 770 sec) [ -16480.1457] [ 2445] [depth= 3] . ( 771 sec) [ -16475.5071] [ 2444] [depth= 1] . ( 781 sec) [ -16443.6971] [ 2440] [depth= 3] . ( 781 sec) [ -16432.6348] [ 2440] [depth= 2] . ( 800 sec) [ -16419.5287] [ 2438] [depth= 2] . ( 801 sec) [ -16413.8595] [ 2437] [depth= 1] . ( 802 sec) [ -16410.8543] [ 2437] [depth= 1] . ( 840 sec) [ -16405.7012] [ 2438] [depth= 1] . ( 873 sec) [ -16381.5386] [ 2437] [depth= 1] . ( 874 sec) [ -16340.6252] [ 2425] [depth= 11] . ( 875 sec) [ -16335.5880] [ 2428] [depth= 1] . ( 875 sec) [ -16329.6989] [ 2425] [depth= 1] . ( 893 sec) [ -16329.0930] [ 2425] [depth= 2] . ( 938 sec) [ -16328.6011] [ 2429] [depth= 1] . ( 959 sec) [ -16327.1333] [ 2428] [depth= 1] . ( 993 sec) [ -16326.5823] [ 2428] [depth= 5] . ( 993 sec) [ -16325.9435] [ 2429] [depth= 1] . ( 1013 sec) [ -16325.8179] [ 2429] [depth= 1] . ( 1014 sec) [ -16325.5769] [ 2429] [depth= 1] . ( 1014 sec) [ -16325.5542] [ 2429] [depth= 1] . ( 1024 sec) [ -16325.1175] [ 2429] [depth= 1] . ( 1053 sec) [ -16325.1029] [ 2429] [depth= 1] . ( 1053 sec) [ -16325.0487] [ 2429] [depth= 1] . ( 1123 sec) [ -16324.1595] [ 2427] [depth= 2] . ( 1124 sec) [ -16323.1032] [ 2428] [depth= 3] . ( 1125 sec) [ -16322.5481] [ 2428] [depth= 1] . ( 1125 sec) [ -16320.5101] [ 2427] [depth= 1] . ( 1126 sec) [ -16320.2298] [ 2427] [depth= 2] . ( 1127 sec) [ -16318.4417] [ 2428] [depth= 1] . ( 1127 sec) [ -16317.6418] [ 2427] [depth= 6] . ( 1128 sec) [ -16317.2985] [ 2427] [depth= 1] . ( 1129 sec) [ -16317.0569] [ 2427] [depth= 1] . ( 1130 sec) [ -16316.2180] [ 2424] [depth= 4] . ( 1131 sec) [ -16313.5823] [ 2425] [depth= 2] . ( 1132 sec) [ -16313.2561] [ 2425] [depth= 3] . ( 1132 sec) [ -16312.8790] [ 2427] [depth= 2] . ( 1133 sec) [ -16309.8318] [ 2427] [depth= 1] . ( 1134 sec) [ -16309.0660] [ 2427] [depth= 6] . ( 1141 sec) [ -16308.9646] [ 2427] [depth= 3] . ( 1142 sec) [ -16308.8497] [ 2427] [depth= 6] . ( 1153 sec) [ -16308.7800] [ 2427] [depth= 1] . ( 1154 sec) [ -16308.7310] [ 2427] [depth= 1] . ( 1163 sec) [ -16307.8914] [ 2427] [depth= 1] . ( 1164 sec) [ -16307.7179] [ 2427] [depth= 1] . ( 1164 sec) [ -16307.6193] [ 2427] [depth= 1] . ( 1186 sec) [ -16306.8790] [ 2427] [depth= 1] . ( 1188 sec) [ -16306.7497] [ 2427] [depth= 2] . ( 1198 sec) [ -16306.7293] [ 2427] [depth= 1] . ( 1217 sec) [ -16306.6162] [ 2427] [depth= 2] . ( 1226 sec) [ -16167.5881] [Branch lengths ] . ( 1235 sec) [ -16164.6243] [GTR parameters ] . ( 1236 sec) [ -16164.5424] [Alpha ][ 0.521612] . ( 1351 sec) [ -16164.4624] [ 2426] [depth= 1] . ( 1430 sec) [ -16164.2363] [ 2425] [depth= 1] . ( 1668 sec) [ -16158.7924] [ 2422] [depth= 1] . ( 1693 sec) [ -16158.6852] [ 2422] [depth= 2] . ( 1771 sec) [ -16158.4164] [ 2420] [depth= 1] . ( 1838 sec) [ -16158.4050] [ 2420] [depth= 1] . ( 1973 sec) [ -16158.1709] [ 2420] [depth= 1] . ( 2001 sec) [ -16158.0392] [ 2420] [depth= 3] . ( 2002 sec) [ -16157.9891] [ 2420] [depth= 4] . ( 2060 sec) [ -16157.7698] [ 2420] [depth= 2] . ( 2154 sec) [ -16156.3763] [ 2420] [depth= 1] . ( 2197 sec) [ -16153.9213] [ 2420] [depth= 6] . ( 2217 sec) [ -16152.6818] [ 2419] [depth= 1] . ( 2282 sec) [ -16152.1474] [ 2418] [depth= 1] . ( 2310 sec) [ -16152.0961] [ 2418] [depth= 1] . ( 2312 sec) [ -16151.0377] [ 2419] [depth= 4] . ( 2322 sec) [ -16142.7485] [ 2416] [depth= 4] . ( 2341 sec) [ -16142.2608] [ 2416] [depth= 1] . ( 2454 sec) [ -16142.2293] [ 2416] [depth= 1] . ( 2497 sec) [ -16134.0143] [ 2412] [depth= 1] . ( 2534 sec) [ -16133.0063] [ 2412] [depth= 1] . ( 2596 sec) [ -16131.2109] [ 2412] [depth= 1] . ( 2601 sec) [ -16130.3069] [ 2411] [depth= 2] . ( 2704 sec) [ -16126.9281] [ 2411] [depth= 3] . ( 2800 sec) [ -16126.9005] [ 2411] [depth= 1] . ( 2881 sec) [ -16126.4009] [ 2411] [depth= 2] . ( 2892 sec) [ -16126.1492] [ 2411] [depth= 3] . ( 2893 sec) [ -16125.5120] [ 2412] [depth= 1] . ( 2894 sec) [ -16124.3210] [ 2411] [depth= 2] . ( 2895 sec) [ -16123.3523] [ 2410] [depth= 6] . ( 2896 sec) [ -16123.1514] [ 2410] [depth= 2] . ( 2896 sec) [ -16122.6232] [ 2410] [depth= 1] . ( 2909 sec) [ -16122.0054] [ 2411] [depth= 5] . ( 2912 sec) [ -16121.6500] [ 2411] [depth= 2] . ( 2913 sec) [ -16121.6282] [ 2411] [depth= 3] . ( 2914 sec) [ -16121.6178] [ 2411] [depth= 2] . ( 2915 sec) [ -16121.0990] [ 2411] [depth= 1] . ( 2937 sec) [ -16120.9238] [ 2411] [depth= 2] . ( 2948 sec) [ -16120.4950] [ 2411] [depth= 1] . ( 2949 sec) [ -16120.4235] [ 2411] [depth= 3] . ( 2949 sec) [ -16120.3997] [ 2411] [depth= 1] . ( 2957 sec) [ -16120.2031] [ 2411] [depth= 2] . ( 2957 sec) [ -16119.9120] [ 2411] [depth= 2] . ( 2989 sec) [ -16119.8218] [ 2411] [depth= 2] . ( 2990 sec) [ -16119.6872] [ 2411] [depth= 1] . ( 2992 sec) [ -16119.6560] [ 2411] [depth= 3] . ( 2993 sec) [ -16119.5869] [ 2411] [depth= 1] . ( 3005 sec) [ -16119.5601] [ 2411] [depth= 1] . ( 3009 sec) [ -16069.4168] [Branch lengths ] . ( 3016 sec) [ -16069.3732] [GTR parameters ] . ( 3017 sec) [ -16066.9697] [Alpha ][ 0.467939] . ( 3139 sec) [ -16066.8094] [ 2412] [depth= 1] . ( 3432 sec) [ -16066.7101] [ 2412] [depth= 1] . ( 3559 sec) [ -16065.9207] [ 2412] [depth= 3] . ( 3560 sec) [ -16065.6386] [ 2409] [depth= 1] . ( 3574 sec) [ -16065.3008] [ 2414] [depth= 2] . ( 3637 sec) [ -16065.1422] [ 2414] [depth= 1] . ( 3812 sec) [ -16056.0831] [ 2413] [depth= 5] . ( 3821 sec) [ -16053.4549] [ 2413] [depth= 3] . ( 3889 sec) [ -16051.6066] [ 2412] [depth= 1] . ( 3899 sec) [ -16051.4165] [ 2413] [depth= 1] . ( 3919 sec) [ -16051.1927] [ 2413] [depth= 1] . ( 4213 sec) [ -16050.6603] [ 2413] [depth= 1] . ( 4219 sec) [ -16050.6004] [ 2413] [depth= 1] . ( 4503 sec) [ -16050.4746] [ 2413] [depth= 1] . ( 4538 sec) [ -16050.4004] [ 2414] [depth= 3] . ( 4540 sec) [ -16050.2899] [ 2414] [depth= 1] . ( 4559 sec) [ -16050.2311] [ 2414] [depth= 1] . ( 4561 sec) [ -16050.0897] [ 2414] [depth= 2] . ( 4567 sec) [ -16049.8705] [ 2414] [depth= 2] . ( 4583 sec) [ -16049.6872] [ 2413] [depth= 3] . ( 4602 sec) [ -16049.6613] [ 2413] [depth= 1] . ( 4607 sec) [ -16049.6256] [ 2413] [depth= 1] . ( 4611 sec) [ -16049.5488] [ 2413] [depth= 2] . ( 4613 sec) [ -16049.5303] [ 2413] [depth= 2] . ( 4636 sec) [ -16049.5035] [ 2413] [depth= 3] . ( 4646 sec) [ -16049.4634] [ 2413] [depth= 2] . ( 4646 sec) [ -16049.4481] [ 2413] [depth= 1] . ( 4665 sec) [ -16021.4722] [Branch lengths ] . ( 4671 sec) [ -16021.3558] [GTR parameters ] . ( 4672 sec) [ -16018.7692] [Alpha ][ 0.420705] . ( 4766 sec) [ -16018.6970] [ 2412] [depth= 1] . ( 5031 sec) [ -16018.6060] [ 2412] [depth= 1] . ( 5085 sec) [ -16018.5891] [ 2412] [depth= 1] . ( 5112 sec) [ -16018.2743] [ 2412] [depth= 1] . ( 6090 sec) [ -16018.2189] [ 2412] [depth= 6] . ( 6124 sec) [ -16018.1750] [ 2412] [depth= 1] . ( 6124 sec) [ -16018.1004] [ 2411] [depth= 2] . ( 6167 sec) [ -16018.0822] [ 2411] [depth= 1] . ( 6232 sec) [ -16018.0559] [ 2411] [depth= 1] . ( 6270 sec) [ -16018.0047] [ 2411] [depth= 3] . ( 6296 sec) [ -16005.6211] [Branch lengths ] . ( 6302 sec) [ -16005.5708] [GTR parameters ] . ( 6303 sec) [ -16004.2296] [Alpha ][ 0.390791] . ( 7560 sec) [ -16004.1947] [ 2411] [depth= 1] . ( 7594 sec) [ -16004.1540] [ 2411] [depth= 2] . ( 7651 sec) [ -16004.1208] [ 2411] [depth= 1] . ( 7671 sec) [ -16004.0977] [ 2411] [depth= 1] . ( 7704 sec) [ -15997.3001] [Branch lengths ] . ( 7707 sec) [ -15997.2812] [GTR parameters ] . ( 7707 sec) [ -15996.6500] [Alpha ][ 0.371948] . ( 8311 sec) [ -15996.6133] [ 2412] [depth= 2] . ( 8828 sec) [ -15996.3056] [ 2412] [depth= 3] . ( 8834 sec) [ -15996.2867] [ 2413] [depth= 2] . ( 8992 sec) [ -15991.5627] [Branch lengths ] . ( 8995 sec) [ -15991.5473] [GTR parameters ] . ( 8995 sec) [ -15991.2004] [Alpha ][ 0.358839] . (10288 sec) [ -15988.7525] [Branch lengths ] . (10305 sec) [ -15988.6283] [ 2412] [depth= 1] . (10437 sec) [ -15988.6033] [ 2412] [depth= 1] . (10588 sec) [ -15986.0845] [Branch lengths ] . (10591 sec) [ -15986.0765] [GTR parameters ] . (10592 sec) [ -15985.6687] [Alpha ][ 0.345355] . (10933 sec) [ -15984.0563] [Branch lengths ] . (10934 sec) [ -15984.0563] [Topology ] . (10940 sec) [ -15983.9147] [Topology ] . (10946 sec) [ -15983.8489] [Topology ] . (10953 sec) [ -15983.8068] [Topology ] . (10959 sec) [ -15983.7786] [Topology ] . (10965 sec) [ -15983.7596] [Topology ] . (10971 sec) [ -15983.7467] [Topology ] . (10974 sec) [ -15983.7414] [GTR parameters ] . (10975 sec) [ -15983.5895] [Alpha ][ 0.337246] . (10975 sec) [ -15983.5895] [Topology ] . (10981 sec) [ -15983.5417] [Topology ] . (10987 sec) [ -15983.5110] [Topology ] . (10994 sec) [ -15983.4901] [Topology ] . (11000 sec) [ -15983.4759] [Topology ] . (11006 sec) [ -15983.4662] [Topology ] . (11013 sec) [ -15983.4595] [Topology ] . (11015 sec) [ -15983.4586] [GTR parameters ] . (11015 sec) [ -15983.4416] [Alpha ][ 0.334575] . (11015 sec) [ -15983.4416] [Topology ] . (11022 sec) [ -15983.4299] [Topology ] . (11028 sec) [ -15983.4222] [Topology ] . (11034 sec) [ -15983.4168] [Topology ] . (11041 sec) [ -15983.4131] [Topology ] . (11047 sec) [ -15983.4105] [Topology ] . (11053 sec) [ -15983.4087] [Topology ] . (11056 sec) [ -15983.4084] [GTR parameters ] . (11056 sec) [ -15983.4042] [Alpha ][ 0.333264] . (11057 sec) [ -15983.4042] [Topology ] . (11063 sec) [ -15983.4012] [Topology ] . (11069 sec) [ -15983.3992] [Topology ] . (11076 sec) [ -15983.3977] [Topology ] . (11082 sec) [ -15983.3967] [Topology ] . (11083 sec) [ -15983.3967] [GTR parameters ] . (11084 sec) [ -15983.3961] [Alpha ][ 0.332748] . (11084 sec) [ -15983.3961] [Topology ] . (11090 sec) [ -15983.3949] [Topology ] . (11096 sec) [ -15983.3941] [Topology ] . (11098 sec) [ -15983.3941] [GTR parameters ] . (11098 sec) [ -15983.3941] [Alpha ][ 0.332415] . (11098 sec) [ -15983.3941] [Topology ] . (11105 sec) [ -15983.3933] [Topology ] . (11106 sec) [ -15983.3933] [GTR parameters ] . (11107 sec) [ -15983.3933] [Alpha ][ 0.332415] . Checking for NNIs, optimizing five branches... . (11155 sec) [ -15983.3930] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15983.392966. . Printing the most likely tree in file 'nucleic_M2587_117x1910_2006.phy_phyml_tree.txt'... . Time used 3h6m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 9047.53user 0.00system 3:06:48elapsed 80%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps