.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M4057_416x4150_2008.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 118 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 3510 patterns found. (out of a total of 4150 sites) . 453 sites without polymorphism (10.92%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 780Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 101 sec) [ -181600.2899] [GTR parameters ] . ( 113 sec) [ -179596.0225] [Alpha ][ 0.500960] . ( 115 sec) [ -179596.0225] [Topology ] . ( 193 sec) [ -172983.3111] [Topology ] . ( 271 sec) [ -170603.5689] [Topology ] . ( 346 sec) [ -169562.4396] [Topology ] . ( 424 sec) [ -168874.0110] [Topology ] . ( 500 sec) [ -168444.2223] [Topology ] . ( 577 sec) [ -168113.3423] [Topology ] . ( 653 sec) [ -167909.5899] [Topology ] . ( 730 sec) [ -167743.7698] [Topology ] . ( 806 sec) [ -167546.8863] [Topology ] . ( 976 sec) [ -167146.1060] [GTR parameters ] . ( 982 sec) [ -166955.5042] [Alpha ][ 0.659486] . ( 984 sec) [ -166955.5042] [Topology ] . ( 1059 sec) [ -166731.1187] [Topology ] . ( 1134 sec) [ -166630.1022] [Topology ] . ( 1209 sec) [ -166546.0418] [Topology ] . ( 1283 sec) [ -166377.7574] [Topology ] . ( 1358 sec) [ -166292.0608] [Topology ] . ( 1432 sec) [ -166214.0811] [Topology ] . ( 1506 sec) [ -166125.3262] [Topology ] . ( 1580 sec) [ -166009.6750] [Topology ] . ( 1654 sec) [ -165918.8113] [Topology ] . ( 1810 sec) [ -165845.7835] [GTR parameters ] . ( 1816 sec) [ -165833.0978] [Alpha ][ 0.628877] . ( 1818 sec) [ -165833.0978] [Topology ] . ( 1892 sec) [ -165756.7962] [Topology ] . ( 1966 sec) [ -165710.0153] [Topology ] . ( 2040 sec) [ -165686.7332] [Topology ] . ( 2116 sec) [ -165663.9956] [Topology ] . ( 2191 sec) [ -165642.2265] [Topology ] . ( 2266 sec) [ -165633.6553] [Topology ] . ( 2342 sec) [ -165630.3527] [Topology ] . ( 2418 sec) [ -165631.0285] [Topology ] . Moving backward . ( 2423 sec) [ -165627.2275] [Topology ] . ( 2572 sec) [ -165624.3967] [GTR parameters ] . ( 2578 sec) [ -165583.0274] [Alpha ][ 0.580586] . ( 2580 sec) [ -165583.0274] [Topology ] . ( 2655 sec) [ -165572.1979] [Topology ] . ( 2731 sec) [ -165567.6815] [Topology ] . ( 2806 sec) [ -165565.5624] [Topology ] . ( 2882 sec) [ -165564.5585] [Topology ] . ( 2958 sec) [ -165564.0218] [Topology ] . ( 3034 sec) [ -165563.7225] [Topology ] . ( 3110 sec) [ -165563.5555] [Topology ] . ( 3186 sec) [ -165563.4631] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3705 sec) [ -165561.4092] [Topology ] . ( 3761 sec) [ -165560.9948] [GTR parameters ] . ( 3768 sec) [ -165554.4450] [Alpha ][ 0.563193] . ( 3770 sec) [ -165554.4450] [Topology ] . ( 3846 sec) [ -165549.8569] [Topology ] . ( 3923 sec) [ -165548.6832] [Topology ] . ( 3999 sec) [ -165548.1347] [Topology ] . ( 4076 sec) [ -165547.8553] [Topology ] . ( 4152 sec) [ -165547.7045] [Topology ] . ( 4229 sec) [ -165547.6178] [Topology ] . ( 4306 sec) [ -165547.5650] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4824 sec) [ -165545.8777] [Topology ] . ( 4879 sec) [ -165545.8343] [GTR parameters ] . ( 4886 sec) [ -165544.1350] [Alpha ][ 0.554913] . ( 4888 sec) [ -165544.1350] [Topology ] . ( 4964 sec) [ -165543.2375] [Topology ] . ( 5039 sec) [ -165542.7570] [Topology ] . ( 5115 sec) [ -165538.7247] [Topology ] . ( 5191 sec) [ -165529.7963] [Topology ] . ( 5266 sec) [ -165526.4013] [Topology ] . ( 5341 sec) [ -165523.5856] [Topology ] . ( 5417 sec) [ -165522.6706] [Topology ] . ( 5493 sec) [ -165521.9573] [Topology ] . ( 5569 sec) [ -165511.3131] [Topology ] . ( 5666 sec) [ -165508.1659] [GTR parameters ] . ( 5673 sec) [ -165505.2231] [Alpha ][ 0.543804] . ( 5675 sec) [ -165505.2231] [Topology ] . ( 5751 sec) [ -165503.7873] [Topology ] . ( 5828 sec) [ -165503.3243] [Topology ] . ( 5904 sec) [ -165503.1331] [Topology ] . ( 5981 sec) [ -165503.0473] [Topology ] . ( 6057 sec) [ -165503.0069] [Topology ] . ( 6132 sec) [ -165502.9871] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6651 sec) [ -165501.5071] [Topology ] . ( 6666 sec) [ -165501.4580] [GTR parameters ] . ( 6672 sec) [ -165500.8280] [Alpha ][ 0.538879] . ( 6675 sec) [ -165500.8280] [Topology ] . ( 6750 sec) [ -165490.5061] [Topology ] . ( 6826 sec) [ -165486.1270] [Topology ] . ( 6902 sec) [ -165477.6074] [Topology ] . ( 6978 sec) [ -165473.3744] [Topology ] . ( 7054 sec) [ -165471.6396] [Topology ] . ( 7130 sec) [ -165471.0641] [Topology ] . ( 7205 sec) [ -165469.7849] [Topology ] . ( 7281 sec) [ -165465.6364] [Topology ] . ( 7357 sec) [ -165464.8217] [Topology ] . Checking for NNIs, optimizing five branches... . ( 7947 sec) [ -165463.7572] [Topology ] . ( 7970 sec) [ -165463.7295] [GTR parameters ] . ( 7976 sec) [ -165463.4446] [Alpha ][ 0.535236] . ( 7979 sec) [ -165463.4446] [Topology ] . ( 8054 sec) [ -165462.1170] [Topology ] . ( 8130 sec) [ -165461.6656] [Topology ] . ( 8206 sec) [ -165457.4694] [Topology ] . ( 8281 sec) [ -165455.0200] [Topology ] . ( 8357 sec) [ -165445.3475] [Topology ] . ( 8433 sec) [ -165440.9099] [Topology ] . ( 8509 sec) [ -165436.6076] [Topology ] . ( 8585 sec) [ -165396.0272] [Topology ] . ( 8661 sec) [ -165374.3195] [Topology ] . ( 8750 sec) [ -165370.5214] [GTR parameters ] . ( 8758 sec) [ -165370.4602] [Alpha ][ 0.533471] . ( 8760 sec) [ -165370.4602] [Topology ] . ( 8836 sec) [ -165369.6145] [Topology ] . ( 8912 sec) [ -165369.3129] [Topology ] . ( 8988 sec) [ -165357.7589] [Topology ] . ( 9064 sec) [ -165355.3334] [Topology ] . ( 9141 sec) [ -165355.0680] [Topology ] . ( 9218 sec) [ -165355.0181] [Topology ] . ( 9294 sec) [ -165355.0077] [Topology ] . ( 9370 sec) [ -165355.0051] [Topology ] . ( 9447 sec) [ -165355.0042] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9961 sec) [ -165354.5859] [Topology ] . ( 9976 sec) [ -165354.5831] [GTR parameters ] . ( 9982 sec) [ -165354.5831] [Alpha ][ 0.533471] . ( 9984 sec) [ -165354.5831] [Topology ] . (10060 sec) [ -165354.3433] [Topology ] . (10136 sec) [ -165354.3089] [Topology ] . (10212 sec) [ -165354.3004] [Topology ] . (10287 sec) [ -165354.2977] [Topology ] . (10363 sec) [ -165354.2966] [Topology ] . (10439 sec) [ -165354.2960] [Topology ] . Checking for NNIs, optimizing five branches... . (10955 sec) [ -165354.1153] [Topology ] . (10970 sec) [ -165354.1139] [GTR parameters ] . (10976 sec) [ -165354.1082] [Alpha ][ 0.532897] . (10978 sec) [ -165354.1082] [Topology ] . (11054 sec) [ -165351.3163] [Topology ] . (11130 sec) [ -165346.1981] [Topology ] . (11207 sec) [ -165343.4009] [Topology ] . (11284 sec) [ -165342.9482] [Topology ] . (11361 sec) [ -165342.8119] [Topology ] . (11438 sec) [ -165342.7875] [Topology ] . (11514 sec) [ -165342.7806] [Topology ] . (11591 sec) [ -165342.7781] [Topology ] . (11668 sec) [ -165342.7770] [Topology ] . Checking for NNIs, optimizing five branches... . (12254 sec) [ -165340.2702] [Topology ] . (12270 sec) [ -165340.2555] [GTR parameters ] . (12276 sec) [ -165340.2540] [Alpha ][ 0.533430] . (12278 sec) [ -165340.2540] [Topology ] . (12354 sec) [ -165339.7646] [Topology ] . (12430 sec) [ -165339.6888] [Topology ] . (12506 sec) [ -165339.6693] [Topology ] . (12583 sec) [ -165339.6632] [Topology ] . (12660 sec) [ -165339.6609] [Topology ] . (12737 sec) [ -165339.6600] [Topology ] . Checking for NNIs, optimizing five branches... . (13251 sec) [ -165339.5323] [Topology ] . (13266 sec) [ -165339.5314] [GTR parameters ] . (13272 sec) [ -165339.5275] [Alpha ][ 0.532896] . (13274 sec) [ -165339.5275] [Topology ] . (13350 sec) [ -165339.5236] [Topology ] . (13426 sec) [ -165339.5224] [Topology ] . (13503 sec) [ -165339.5218] [Topology ] . Checking for NNIs, optimizing five branches... . (14013 sec) [ -165339.4891] [Topology ] . (14069 sec) [ -165339.4874] [GTR parameters ] . (14074 sec) [ -165339.4874] [Alpha ][ 0.532896] . (14077 sec) [ -165339.4874] [Topology ] . (14153 sec) [ -165339.3142] [Topology ] . (14229 sec) [ -165339.2914] [Topology ] . (14305 sec) [ -165339.2871] [Topology ] . (14381 sec) [ -165339.2860] [Topology ] . (14458 sec) [ -165339.2857] [Topology ] . Checking for NNIs, optimizing five branches... . (14968 sec) [ -165339.2703] [Topology ] . (14984 sec) [ -165339.2698] [GTR parameters ] . (14990 sec) [ -165339.2698] [Alpha ][ 0.532896] . (14992 sec) [ -165339.2698] [Topology ] . (15069 sec) [ -165338.1343] [Topology ] . (15145 sec) [ -165337.5825] [Topology ] . (15222 sec) [ -165337.5001] [Topology ] . (15299 sec) [ -165337.4795] [Topology ] . (15376 sec) [ -165337.4733] [Topology ] . (15453 sec) [ -165337.4713] [Topology ] . (15530 sec) [ -165337.4705] [Topology ] . Checking for NNIs, optimizing five branches... . (16043 sec) [ -165337.3739] [Topology ] . (16058 sec) [ -165337.3720] [GTR parameters ] . (16064 sec) [ -165337.3671] [Alpha ][ 0.532355] . (16066 sec) [ -165337.3671] [Topology ] . (16142 sec) [ -165333.8663] [Topology ] . (16218 sec) [ -165333.0461] [Topology ] . (16295 sec) [ -165330.0377] [Topology ] . (16371 sec) [ -165327.1840] [Topology ] . (16447 sec) [ -165324.6938] [Topology ] . (16523 sec) [ -165324.2269] [Topology ] . (16600 sec) [ -165324.1376] [Topology ] . (16676 sec) [ -165324.1189] [Topology ] . (16752 sec) [ -165324.1148] [Topology ] . Checking for NNIs, optimizing five branches... . (17269 sec) [ -165324.0999] [Topology ] . (17284 sec) [ -165324.0960] [GTR parameters ] . (17290 sec) [ -165324.0913] [Alpha ][ 0.531823] . (17292 sec) [ -165324.0913] [Topology ] . (17369 sec) [ -165324.0661] [Topology ] . (17445 sec) [ -165324.0578] [Topology ] . (17522 sec) [ -165324.0537] [Topology ] . (17598 sec) [ -165324.0514] [Topology ] . (17675 sec) [ -165324.0501] [Topology ] . (17751 sec) [ -165324.0494] [Topology ] . Checking for NNIs, optimizing five branches... . (18282 sec) [ -165324.0488] [GTR parameters ] . (18288 sec) [ -165324.0449] [Alpha ][ 0.531291] . (18290 sec) [ -165324.0449] [Topology ] . (18367 sec) [ -165324.0415] [Topology ] . (18444 sec) [ -165324.0397] [Topology ] . (18520 sec) [ -165324.0386] [Topology ] . (18597 sec) [ -165324.0379] [Topology ] . Checking for NNIs, optimizing five branches... . (19110 sec) [ -165324.0118] [Topology ] . (19125 sec) [ -165324.0021] [GTR parameters ] . (19131 sec) [ -165324.0021] [Alpha ][ 0.531291] . (19133 sec) [ -165324.0021] [Topology ] . (19210 sec) [ -165322.7958] [Topology ] . (19287 sec) [ -165322.2573] [Topology ] . (19364 sec) [ -165321.8910] [Topology ] . (19441 sec) [ -165321.8197] [Topology ] . (19517 sec) [ -165321.7976] [Topology ] . (19593 sec) [ -165321.7900] [Topology ] . (19670 sec) [ -165321.7873] [Topology ] . (19746 sec) [ -165321.7863] [Topology ] . Checking for NNIs, optimizing five branches... . (20259 sec) [ -165321.7656] [Topology ] . (20321 sec) [ -165321.7600] [GTR parameters ] . (20327 sec) [ -165321.7385] [Alpha ][ 0.530247] . (20329 sec) [ -165321.7385] [Topology ] . (20405 sec) [ -165314.2876] [Topology ] . (20481 sec) [ -165311.8168] [Topology ] . (20558 sec) [ -165307.6001] [Topology ] . (20634 sec) [ -165296.5533] [Topology ] . (20711 sec) [ -165295.4591] [Topology ] . (20787 sec) [ -165293.9520] [Topology ] . (20863 sec) [ -165289.0242] [Topology ] . (20940 sec) [ -165287.5280] [Topology ] . (21016 sec) [ -165287.1914] [Topology ] . Checking for NNIs, optimizing five branches... . (21626 sec) [ -165287.0849] [GTR parameters ] . (21632 sec) [ -165287.0716] [Alpha ][ 0.529388] . (21634 sec) [ -165287.0716] [Topology ] . (21710 sec) [ -165287.0343] [Topology ] . (21787 sec) [ -165287.0216] [Topology ] . (21863 sec) [ -165287.0171] [Topology ] . (21939 sec) [ -165287.0154] [Topology ] . (22016 sec) [ -165287.0148] [Topology ] . Checking for NNIs, optimizing five branches... . (22540 sec) [ -165287.0147] [GTR parameters ] . (22546 sec) [ -165287.0147] [Alpha ][ 0.529388] . (22548 sec) [ -165287.0147] [Topology ] . (22625 sec) [ -165287.0144] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -165287.014418. . Printing the most likely tree in file 'nucleic_M4057_416x4150_2008.phy_phyml_tree.txt'... . Time used 6h34m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 23518.48user 0.00system 6:35:02elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps