.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_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... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -15009.3920] [GTR parameters ] . ( 4 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 9 sec) [ -14724.6451] [ 2562] [depth= 2] . ( 9 sec) [ -14721.3879] [ 2562] [depth= 1] . ( 9 sec) [ -14721.0926] [ 2562] [depth= 1] . ( 21 sec) [ -14717.3225] [ 2562] [depth= 2] . ( 21 sec) [ -14714.6002] [ 2561] [depth= 2] . ( 24 sec) [ -14714.3106] [ 2561] [depth= 1] . ( 24 sec) [ -14713.7025] [ 2562] [depth= 1] . ( 25 sec) [ -14713.3967] [ 2561] [depth= 1] . ( 33 sec) [ -14704.7688] [ 2559] [depth= 2] . ( 42 sec) [ -14704.3651] [ 2563] [depth= 1] . ( 43 sec) [ -14695.9944] [ 2562] [depth= 1] . ( 43 sec) [ -14695.9146] [ 2563] [depth= 1] . ( 44 sec) [ -14695.4095] [ 2570] [depth= 2] . ( 44 sec) [ -14677.4597] [ 2564] [depth= 2] . ( 44 sec) [ -14672.0703] [ 2562] [depth= 1] . ( 46 sec) [ -14671.1751] [ 2563] [depth= 1] . ( 46 sec) [ -14667.4994] [ 2562] [depth= 1] . ( 49 sec) [ -14664.9989] [ 2568] [depth= 1] . ( 49 sec) [ -14658.2309] [ 2562] [depth= 1] . ( 49 sec) [ -14656.8572] [ 2561] [depth= 1] . ( 50 sec) [ -14651.0694] [ 2570] [depth= 5] . ( 50 sec) [ -14646.5716] [ 2566] [depth= 1] . ( 50 sec) [ -14631.7056] [ 2571] [depth= 7] . ( 50 sec) [ -14621.0240] [ 2561] [depth= 7] . ( 50 sec) [ -14616.6002] [ 2562] [depth= 1] . ( 50 sec) [ -14616.1341] [ 2561] [depth= 1] . ( 50 sec) [ -14609.4997] [ 2562] [depth= 1] . ( 50 sec) [ -14607.5008] [ 2561] [depth= 1] . ( 50 sec) [ -14605.1278] [ 2561] [depth= 1] . ( 50 sec) [ -14600.6419] [ 2561] [depth= 1] . ( 52 sec) [ -14596.6883] [ 2558] [depth= 1] . ( 52 sec) [ -14592.5409] [ 2562] [depth= 2] . ( 52 sec) [ -14585.5921] [ 2559] [depth= 2] . ( 52 sec) [ -14580.8242] [ 2562] [depth= 1] . ( 52 sec) [ -14579.5596] [ 2559] [depth= 1] . ( 54 sec) [ -14576.0489] [ 2563] [depth= 1] . ( 56 sec) [ -14571.4297] [ 2559] [depth= 2] . ( 56 sec) [ -14560.6452] [ 2557] [depth= 2] . ( 58 sec) [ -14558.6024] [ 2553] [depth= 1] . ( 59 sec) [ -14555.4855] [ 2552] [depth= 1] . ( 59 sec) [ -14555.2129] [ 2554] [depth= 3] . ( 59 sec) [ -14550.5865] [ 2555] [depth= 1] . ( 59 sec) [ -14547.6996] [ 2555] [depth= 1] . ( 59 sec) [ -14547.5852] [ 2561] [depth= 1] . ( 59 sec) [ -14544.5603] [ 2560] [depth= 1] . ( 61 sec) [ -14538.7479] [ 2555] [depth= 5] . ( 65 sec) [ -14526.6492] [ 2557] [depth= 3] . ( 65 sec) [ -14526.1360] [ 2555] [depth= 1] . ( 66 sec) [ -14522.8896] [ 2553] [depth= 1] . ( 66 sec) [ -14522.6007] [ 2554] [depth= 1] . ( 68 sec) [ -14515.7392] [ 2553] [depth= 1] . ( 68 sec) [ -14506.3831] [ 2549] [depth= 2] . ( 70 sec) [ -14505.8481] [ 2548] [depth= 1] . ( 70 sec) [ -14505.6498] [ 2549] [depth= 1] . ( 71 sec) [ -14505.3199] [ 2551] [depth= 1] . ( 73 sec) [ -14504.8100] [ 2557] [depth= 1] . ( 74 sec) [ -14504.1923] [ 2557] [depth= 1] . ( 80 sec) [ -14501.8479] [ 2555] [depth= 2] . ( 81 sec) [ -14501.7409] [ 2555] [depth= 1] . ( 81 sec) [ -14500.9857] [ 2556] [depth= 1] . ( 81 sec) [ -14500.9726] [ 2556] [depth= 1] . ( 83 sec) [ -14500.9430] [ 2557] [depth= 1] . ( 88 sec) [ -14499.7126] [ 2556] [depth= 1] . ( 90 sec) [ -14498.9923] [ 2558] [depth= 1] . ( 90 sec) [ -14497.4152] [ 2559] [depth= 1] . ( 93 sec) [ -14490.7591] [ 2551] [depth= 2] . ( 97 sec) [ -14490.3826] [ 2547] [depth= 3] . ( 97 sec) [ -14489.9830] [ 2546] [depth= 1] . ( 99 sec) [ -14489.5864] [ 2547] [depth= 2] . ( 104 sec) [ -14489.5540] [ 2550] [depth= 1] . ( 108 sec) [ -14444.1586] [Branch lengths ] . ( 110 sec) [ -14442.9831] [GTR parameters ] . ( 110 sec) [ -14349.7576] [Alpha ][ 0.272622] . ( 150 sec) [ -14349.6263] [ 2547] [depth= 1] . ( 187 sec) [ -14349.5040] [ 2550] [depth= 7] . ( 192 sec) [ -14349.2815] [ 2552] [depth= 6] . ( 195 sec) [ -14349.1283] [ 2556] [depth= 1] . ( 195 sec) [ -14347.5979] [ 2552] [depth= 1] . ( 206 sec) [ -14347.5522] [ 2551] [depth= 1] . ( 214 sec) [ -14347.4574] [ 2550] [depth= 1] . ( 227 sec) [ -14346.4448] [ 2548] [depth= 2] . ( 239 sec) [ -14346.4059] [ 2548] [depth= 1] . ( 264 sec) [ -14346.0925] [ 2554] [depth= 3] . ( 268 sec) [ -14346.0199] [ 2555] [depth= 1] . ( 268 sec) [ -14345.9310] [ 2555] [depth= 1] . ( 295 sec) [ -14345.8181] [ 2556] [depth= 1] . ( 295 sec) [ -14337.9092] [ 2546] [depth= 9] . ( 304 sec) [ -14331.8639] [Branch lengths ] . ( 306 sec) [ -14331.4485] [GTR parameters ] . ( 307 sec) [ -14331.4478] [Alpha ][ 0.273022] . ( 312 sec) [ -14331.2345] [ 2547] [depth= 2] . ( 444 sec) [ -14329.8439] [ 2548] [depth= 1] . ( 518 sec) [ -14329.2775] [ 2548] [depth= 5] . ( 519 sec) [ -14328.5051] [Branch lengths ] . ( 521 sec) [ -14328.4794] [GTR parameters ] . ( 521 sec) [ -14328.4740] [Alpha ][ 0.274182] . ( 740 sec) [ -14328.3232] [Branch lengths ] . ( 812 sec) [ -14328.2337] [Branch lengths ] . ( 812 sec) [ -14328.2337] [Topology ] . ( 813 sec) [ -14328.1039] [Topology ] . ( 815 sec) [ -14328.0727] [Topology ] . ( 817 sec) [ -14328.0632] [Topology ] . ( 818 sec) [ -14328.0601] [Topology ] . ( 820 sec) [ -14328.0590] [Topology ] . ( 822 sec) [ -14328.0585] [Topology ] . ( 823 sec) [ -14328.0566] [GTR parameters ] . ( 823 sec) [ -14328.0427] [Alpha ][ 0.276069] . ( 823 sec) [ -14328.0427] [Topology ] . ( 825 sec) [ -14328.0411] [Topology ] . ( 826 sec) [ -14328.0402] [Topology ] . ( 828 sec) [ -14328.0400] [GTR parameters ] . ( 828 sec) [ -14328.0400] [Alpha ][ 0.276069] . ( 828 sec) [ -14328.0400] [Topology ] . ( 830 sec) [ -14328.0395] [Topology ] . ( 830 sec) [ -14328.0395] [GTR parameters ] . ( 830 sec) [ -14328.0394] [Alpha ][ 0.276345] . Checking for NNIs, optimizing five branches... . ( 843 sec) [ -14327.9303] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14327.930316. . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Time used 0h14m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 850.11user 0.00system 14:16.31elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps