.......................... 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 (RAxML_result.nucleic_M2945_62x1271_2006.phy_RAXML_CAT)" . 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) [ -36779.3441] [Branch lengths ] . ( 6 sec) [ -35660.5155] [GTR parameters ] . ( 7 sec) [ -35235.2376] [Alpha ][ 0.500960] . ( 8 sec) [ -35169.5827] [Branch lengths ] . ( 12 sec) [ -35156.0736] [GTR parameters ] . ( 12 sec) [ -35149.1858] [Alpha ][ 0.456268] . ( 13 sec) [ -35139.1000] [Branch lengths ] . ( 15 sec) [ -35137.9748] [GTR parameters ] . ( 16 sec) [ -35137.7756] [Alpha ][ 0.448975] . ( 17 sec) [ -35130.8893] [Branch lengths ] . ( 19 sec) [ -35130.4421] [GTR parameters ] . ( 19 sec) [ -35130.3269] [Alpha ][ 0.443589] . ( 20 sec) [ -35125.8749] [Branch lengths ] . ( 23 sec) [ -35125.6098] [GTR parameters ] . ( 23 sec) [ -35125.5405] [Alpha ][ 0.439512] . ( 24 sec) [ -35122.6523] [Branch lengths ] . ( 27 sec) [ -35122.4881] [GTR parameters ] . ( 28 sec) [ -35122.4240] [Alpha ][ 0.435676] . ( 28 sec) [ -35120.3004] [Branch lengths ] . ( 31 sec) [ -35120.1935] [GTR parameters ] . ( 31 sec) [ -35120.1460] [Alpha ][ 0.432433] . ( 32 sec) [ -35118.7821] [Branch lengths ] . ( 34 sec) [ -35118.7162] [GTR parameters ] . ( 34 sec) [ -35118.6746] [Alpha ][ 0.429445] . ( 35 sec) [ -35117.7406] [Branch lengths ] . ( 36 sec) [ -35117.7020] [GTR parameters ] . ( 36 sec) [ -35117.6726] [Alpha ][ 0.426963] . ( 37 sec) [ -35117.1243] [Branch lengths ] . ( 40 sec) [ -35117.0936] [GTR parameters ] . ( 40 sec) [ -35117.0744] [Alpha ][ 0.424978] . ( 41 sec) [ -35116.7212] [Branch lengths ] . ( 43 sec) [ -35116.7094] [GTR parameters ] . ( 43 sec) [ -35116.6968] [Alpha ][ 0.423383] . ( 44 sec) [ -35116.5014] [Branch lengths ] . ( 45 sec) [ -35116.4932] [GTR parameters ] . ( 46 sec) [ -35116.4852] [Alpha ][ 0.422119] . ( 47 sec) [ -35116.3645] [Branch lengths ] . ( 48 sec) [ -35116.3616] [GTR parameters ] . ( 49 sec) [ -35116.3577] [Alpha ][ 0.421231] . ( 50 sec) [ -35116.2949] [Branch lengths ] . ( 50 sec) [ -35116.2921] [GTR parameters ] . ( 50 sec) [ -35116.2895] [Alpha ][ 0.420514] . ( 51 sec) [ -35116.2530] [Branch lengths ] . ( 53 sec) [ -35116.2515] [GTR parameters ] . ( 53 sec) [ -35116.2502] [Alpha ][ 0.419995] . ( 54 sec) [ -35116.2310] [Branch lengths ] . ( 55 sec) [ -35116.2301] [GTR parameters ] . ( 55 sec) [ -35116.2293] [Alpha ][ 0.419575] . ( 56 sec) [ -35116.2183] [Branch lengths ] . ( 56 sec) [ -35116.2178] [GTR parameters ] . ( 57 sec) [ -35116.2176] [Alpha ][ 0.419156] . ( 58 sec) [ -35116.2116] [Branch lengths ] . ( 59 sec) [ -35116.2111] [GTR parameters ] . ( 59 sec) [ -35116.2111] [Alpha ][ 0.419156] . ( 60 sec) [ -35116.2079] [Branch lengths ] . ( 60 sec) [ -35116.2078] [GTR parameters ] . ( 61 sec) [ -35116.2077] [Alpha ][ 0.418737] . ( 62 sec) [ -35116.2056] [Branch lengths ] . ( 62 sec) [ -35116.2056] [GTR parameters ] . ( 62 sec) [ -35116.2056] [Alpha ][ 0.418737] . ( 63 sec) [ -35116.2045] [Branch lengths ] . ( 64 sec) [ -35116.2045] [GTR parameters ] . ( 64 sec) [ -35116.2045] [Alpha ][ 0.418737] . ( 65 sec) [ -35116.2040] [Branch lengths ] . ( 66 sec) [ -35116.2040] [GTR parameters ] . ( 66 sec) [ -35116.2040] [Alpha ][ 0.418737] . ( 67 sec) [ -35116.2040] [GTR parameters ] . ( 67 sec) [ -35116.2040] [Alpha ][ 0.418737] . Log likelihood of the current tree: -35116.203975. . 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 0h1m32s 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)