.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2945_62x1271_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_M2945_62x1271_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 935 patterns found. (out of a total of 1271 sites) . 411 sites without polymorphism (32.34%). . Reading tree... . This analysis requires at least 30Mo of memory space. . ( 1 sec) [ -36647.3866] [Branch lengths ] . ( 5 sec) [ -35601.8924] [GTR parameters ] . ( 5 sec) [ -35255.7723] [Alpha ][ 0.500960] . ( 6 sec) [ -35223.6650] [Branch lengths ] . ( 11 sec) [ -35207.2336] [GTR parameters ] . ( 11 sec) [ -35202.9549] [Alpha ][ 0.462383] . ( 12 sec) [ -35184.9872] [Branch lengths ] . ( 15 sec) [ -35182.2150] [GTR parameters ] . ( 15 sec) [ -35182.2147] [Alpha ][ 0.461921] . ( 16 sec) [ -35168.5024] [Branch lengths ] . ( 18 sec) [ -35167.3770] [GTR parameters ] . ( 19 sec) [ -35167.3508] [Alpha ][ 0.459150] . ( 20 sec) [ -35155.4668] [Branch lengths ] . ( 23 sec) [ -35154.7303] [GTR parameters ] . ( 23 sec) [ -35154.6385] [Alpha ][ 0.454171] . ( 24 sec) [ -35147.6480] [Branch lengths ] . ( 26 sec) [ -35147.2501] [GTR parameters ] . ( 27 sec) [ -35147.1405] [Alpha ][ 0.448911] . ( 28 sec) [ -35142.4092] [Branch lengths ] . ( 29 sec) [ -35142.1410] [GTR parameters ] . ( 29 sec) [ -35142.0534] [Alpha ][ 0.444341] . ( 30 sec) [ -35139.3290] [Branch lengths ] . ( 32 sec) [ -35139.1816] [GTR parameters ] . ( 33 sec) [ -35139.1129] [Alpha ][ 0.440385] . ( 33 sec) [ -35137.1657] [Branch lengths ] . ( 36 sec) [ -35137.0690] [GTR parameters ] . ( 36 sec) [ -35137.0167] [Alpha ][ 0.436997] . ( 37 sec) [ -35135.8676] [Branch lengths ] . ( 39 sec) [ -35135.8144] [GTR parameters ] . ( 39 sec) [ -35135.7764] [Alpha ][ 0.434151] . ( 40 sec) [ -35134.9664] [Branch lengths ] . ( 43 sec) [ -35134.9306] [GTR parameters ] . ( 43 sec) [ -35134.9044] [Alpha ][ 0.431816] . ( 44 sec) [ -35134.4270] [Branch lengths ] . ( 47 sec) [ -35134.4077] [GTR parameters ] . ( 47 sec) [ -35134.3901] [Alpha ][ 0.429917] . ( 48 sec) [ -35134.0597] [Branch lengths ] . ( 50 sec) [ -35134.0456] [GTR parameters ] . ( 50 sec) [ -35134.0334] [Alpha ][ 0.428349] . ( 51 sec) [ -35133.8415] [Branch lengths ] . ( 53 sec) [ -35133.8341] [GTR parameters ] . ( 53 sec) [ -35133.8270] [Alpha ][ 0.427153] . ( 54 sec) [ -35133.6973] [Branch lengths ] . ( 55 sec) [ -35133.6909] [GTR parameters ] . ( 55 sec) [ -35133.6854] [Alpha ][ 0.426107] . ( 57 sec) [ -35133.6107] [Branch lengths ] . ( 59 sec) [ -35133.6077] [GTR parameters ] . ( 59 sec) [ -35133.6046] [Alpha ][ 0.425318] . ( 60 sec) [ -35133.5541] [Branch lengths ] . ( 61 sec) [ -35133.5522] [GTR parameters ] . ( 61 sec) [ -35133.5502] [Alpha ][ 0.424674] . ( 62 sec) [ -35133.5220] [Branch lengths ] . ( 64 sec) [ -35133.5207] [GTR parameters ] . ( 64 sec) [ -35133.5196] [Alpha ][ 0.424198] . ( 65 sec) [ -35133.5007] [Branch lengths ] . ( 66 sec) [ -35133.5000] [GTR parameters ] . ( 66 sec) [ -35133.4993] [Alpha ][ 0.423773] . ( 67 sec) [ -35133.4887] [Branch lengths ] . ( 68 sec) [ -35133.4884] [GTR parameters ] . ( 68 sec) [ -35133.4881] [Alpha ][ 0.423350] . ( 69 sec) [ -35133.4808] [Branch lengths ] . ( 70 sec) [ -35133.4805] [GTR parameters ] . ( 70 sec) [ -35133.4805] [Alpha ][ 0.423350] . ( 71 sec) [ -35133.4769] [Branch lengths ] . ( 72 sec) [ -35133.4768] [GTR parameters ] . ( 73 sec) [ -35133.4766] [Alpha ][ 0.422926] . ( 73 sec) [ -35133.4738] [Branch lengths ] . ( 74 sec) [ -35133.4737] [GTR parameters ] . ( 75 sec) [ -35133.4737] [Alpha ][ 0.422926] . ( 76 sec) [ -35133.4723] [Branch lengths ] . ( 76 sec) [ -35133.4723] [GTR parameters ] . ( 76 sec) [ -35133.4723] [Alpha ][ 0.422926] . ( 77 sec) [ -35133.4716] [Branch lengths ] . ( 78 sec) [ -35133.4716] [GTR parameters ] . ( 78 sec) [ -35133.4716] [Alpha ][ 0.422926] . ( 79 sec) [ -35133.4716] [GTR parameters ] . ( 79 sec) [ -35133.4716] [Alpha ][ 0.422926] . Log likelihood of the current tree: -35133.471561. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Time used 0h1m44s 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)