.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2707_115x1677_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Compute approximate likelihood ratio test : yes (SH-like branch supports) . 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 : no . Evaluted tree : file "user tree (nucleic_M2707_115x1677_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 759 patterns found. (out of a total of 1677 sites) . 924 sites without polymorphism (55.10%). . Reading tree... . This analysis requires at least 46Mo of memory space. . ( 2 sec) [ -10282.2908] [Branch lengths ] . ( 12 sec) [ -10109.0609] [GTR parameters ] . ( 13 sec) [ -9949.0076] [Alpha ][ 0.500960] . ( 14 sec) [ -9920.0643] [Branch lengths ] . ( 20 sec) [ -9918.4781] [GTR parameters ] . ( 21 sec) [ -9857.6264] [Alpha ][ 0.274079] . ( 22 sec) [ -9831.5239] [Branch lengths ] . ( 31 sec) [ -9829.9917] [GTR parameters ] . ( 32 sec) [ -9828.9511] [Alpha ][ 0.255480] . ( 33 sec) [ -9812.2468] [Branch lengths ] . ( 40 sec) [ -9811.2886] [GTR parameters ] . ( 40 sec) [ -9811.0152] [Alpha ][ 0.247022] . ( 42 sec) [ -9798.9399] [Branch lengths ] . ( 48 sec) [ -9798.6164] [GTR parameters ] . ( 49 sec) [ -9798.0171] [Alpha ][ 0.235476] . ( 50 sec) [ -9789.9616] [Branch lengths ] . ( 54 sec) [ -9789.7426] [GTR parameters ] . ( 54 sec) [ -9789.2688] [Alpha ][ 0.225865] . ( 56 sec) [ -9784.0865] [Branch lengths ] . ( 60 sec) [ -9783.9804] [GTR parameters ] . ( 61 sec) [ -9783.5954] [Alpha ][ 0.217641] . ( 62 sec) [ -9780.7576] [Branch lengths ] . ( 67 sec) [ -9780.6722] [GTR parameters ] . ( 67 sec) [ -9780.4619] [Alpha ][ 0.211791] . ( 68 sec) [ -9778.6648] [Branch lengths ] . ( 70 sec) [ -9778.6256] [GTR parameters ] . ( 71 sec) [ -9778.4737] [Alpha ][ 0.206975] . ( 72 sec) [ -9777.3557] [Branch lengths ] . ( 76 sec) [ -9777.3251] [GTR parameters ] . ( 77 sec) [ -9777.2331] [Alpha ][ 0.203331] . ( 78 sec) [ -9776.5598] [Branch lengths ] . ( 81 sec) [ -9776.5449] [GTR parameters ] . ( 81 sec) [ -9776.4822] [Alpha ][ 0.200387] . ( 83 sec) [ -9776.0813] [Branch lengths ] . ( 88 sec) [ -9776.0651] [GTR parameters ] . ( 89 sec) [ -9776.0321] [Alpha ][ 0.198306] . ( 90 sec) [ -9775.8063] [Branch lengths ] . ( 93 sec) [ -9775.8004] [GTR parameters ] . ( 94 sec) [ -9775.7791] [Alpha ][ 0.196674] . ( 95 sec) [ -9775.6560] [Branch lengths ] . ( 98 sec) [ -9775.6523] [GTR parameters ] . ( 98 sec) [ -9775.6410] [Alpha ][ 0.195523] . ( 99 sec) [ -9775.5709] [Branch lengths ] . ( 103 sec) [ -9775.5697] [GTR parameters ] . ( 103 sec) [ -9775.5626] [Alpha ][ 0.194451] . ( 104 sec) [ -9775.5224] [Branch lengths ] . ( 108 sec) [ -9775.5207] [GTR parameters ] . ( 108 sec) [ -9775.5183] [Alpha ][ 0.193806] . ( 110 sec) [ -9775.4942] [Branch lengths ] . ( 111 sec) [ -9775.4941] [GTR parameters ] . ( 111 sec) [ -9775.4929] [Alpha ][ 0.193333] . ( 113 sec) [ -9775.4803] [Branch lengths ] . ( 116 sec) [ -9775.4787] [GTR parameters ] . ( 116 sec) [ -9775.4781] [Alpha ][ 0.192966] . ( 117 sec) [ -9775.4699] [Branch lengths ] . ( 120 sec) [ -9775.4697] [GTR parameters ] . ( 121 sec) [ -9775.4694] [Alpha ][ 0.192692] . ( 122 sec) [ -9775.4647] [Branch lengths ] . ( 123 sec) [ -9775.4647] [GTR parameters ] . ( 123 sec) [ -9775.4645] [Alpha ][ 0.192495] . ( 125 sec) [ -9775.4619] [Branch lengths ] . ( 128 sec) [ -9775.4616] [GTR parameters ] . ( 128 sec) [ -9775.4616] [Alpha ][ 0.192303] . ( 129 sec) [ -9775.4598] [Branch lengths ] . ( 130 sec) [ -9775.4598] [GTR parameters ] . ( 131 sec) [ -9775.4598] [Alpha ][ 0.192303] . ( 132 sec) [ -9775.4589] [Branch lengths ] . ( 132 sec) [ -9775.4589] [GTR parameters ] . ( 133 sec) [ -9775.4589] [Alpha ][ 0.192110] . ( 135 sec) [ -9775.4589] [GTR parameters ] . ( 135 sec) [ -9775.4589] [Alpha ][ 0.192110] . Log likelihood of the current tree: -9775.458881. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2707_115x1677_2006.phy_phyml_tree.txt'... . Time used 0h2m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo java.lang.NullPointerException at java.io.FileInputStream.(FileInputStream.java:103) at java.io.FileReader.(FileReader.java:55) at Recomp.(Recomp.java:114) at Recomp.main(Recomp.java:52)