.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2623_139x1044_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_M2623_139x1044_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 959 patterns found. (out of a total of 1044 sites) . 202 sites without polymorphism (19.35%). . Reading tree... . This analysis requires at least 71Mo of memory space. . ( 3 sec) [ -47921.5880] [Branch lengths ] . ( 5 sec) [ -46843.2938] [GTR parameters ] . ( 6 sec) [ -46568.4284] [Alpha ][ 0.558359] . ( 8 sec) [ -46533.9831] [Branch lengths ] . ( 22 sec) [ -46026.6244] [GTR parameters ] . ( 22 sec) [ -46022.2865] [Alpha ][ 0.518765] . ( 24 sec) [ -45986.7039] [Branch lengths ] . ( 31 sec) [ -45984.1633] [GTR parameters ] . ( 31 sec) [ -45984.1143] [Alpha ][ 0.522779] . ( 33 sec) [ -45972.2055] [Branch lengths ] . ( 41 sec) [ -45971.9062] [GTR parameters ] . ( 41 sec) [ -45971.9017] [Alpha ][ 0.523974] . ( 43 sec) [ -45965.7585] [Branch lengths ] . ( 52 sec) [ -45965.6254] [GTR parameters ] . ( 53 sec) [ -45965.5801] [Alpha ][ 0.527700] . ( 55 sec) [ -45962.4594] [Branch lengths ] . ( 62 sec) [ -45962.3871] [GTR parameters ] . ( 62 sec) [ -45962.3871] [Alpha ][ 0.527700] . ( 64 sec) [ -45960.5166] [Branch lengths ] . ( 70 sec) [ -45960.4765] [GTR parameters ] . ( 70 sec) [ -45960.4714] [Alpha ][ 0.528903] . ( 72 sec) [ -45959.5117] [Branch lengths ] . ( 76 sec) [ -45959.4903] [GTR parameters ] . ( 76 sec) [ -45959.4892] [Alpha ][ 0.528346] . ( 78 sec) [ -45958.9116] [Branch lengths ] . ( 81 sec) [ -45958.9005] [GTR parameters ] . ( 82 sec) [ -45958.9005] [Alpha ][ 0.528346] . ( 84 sec) [ -45958.6134] [Branch lengths ] . ( 86 sec) [ -45958.6062] [GTR parameters ] . ( 87 sec) [ -45958.6062] [Alpha ][ 0.528346] . ( 89 sec) [ -45958.4335] [Branch lengths ] . ( 91 sec) [ -45958.4308] [GTR parameters ] . ( 91 sec) [ -45958.4308] [Alpha ][ 0.528346] . ( 93 sec) [ -45958.3446] [Branch lengths ] . ( 95 sec) [ -45958.3427] [GTR parameters ] . ( 96 sec) [ -45958.3425] [Alpha ][ 0.527818] . ( 98 sec) [ -45958.2904] [Branch lengths ] . ( 100 sec) [ -45958.2892] [GTR parameters ] . ( 100 sec) [ -45958.2892] [Alpha ][ 0.527818] . ( 102 sec) [ -45958.2621] [Branch lengths ] . ( 104 sec) [ -45958.2617] [GTR parameters ] . ( 105 sec) [ -45958.2617] [Alpha ][ 0.527818] . ( 107 sec) [ -45958.2452] [Branch lengths ] . ( 108 sec) [ -45958.2448] [GTR parameters ] . ( 109 sec) [ -45958.2448] [Alpha ][ 0.527818] . ( 111 sec) [ -45958.2360] [Branch lengths ] . ( 112 sec) [ -45958.2356] [GTR parameters ] . ( 113 sec) [ -45958.2356] [Alpha ][ 0.527818] . ( 115 sec) [ -45958.2298] [Branch lengths ] . ( 116 sec) [ -45958.2296] [GTR parameters ] . ( 117 sec) [ -45958.2296] [Alpha ][ 0.527818] . ( 119 sec) [ -45958.2259] [Branch lengths ] . ( 121 sec) [ -45958.2258] [GTR parameters ] . ( 121 sec) [ -45958.2258] [Alpha ][ 0.527818] . ( 123 sec) [ -45958.2234] [Branch lengths ] . ( 124 sec) [ -45958.2234] [GTR parameters ] . ( 124 sec) [ -45958.2234] [Alpha ][ 0.527818] . ( 127 sec) [ -45958.2217] [Branch lengths ] . ( 128 sec) [ -45958.2217] [GTR parameters ] . ( 128 sec) [ -45958.2217] [Alpha ][ 0.527818] . ( 130 sec) [ -45958.2206] [Branch lengths ] . ( 132 sec) [ -45958.2205] [GTR parameters ] . ( 133 sec) [ -45958.2205] [Alpha ][ 0.527818] . ( 135 sec) [ -45958.2197] [Branch lengths ] . ( 136 sec) [ -45958.2197] [GTR parameters ] . ( 136 sec) [ -45958.2197] [Alpha ][ 0.527818] . ( 138 sec) [ -45958.2196] [GTR parameters ] . ( 139 sec) [ -45958.2196] [Alpha ][ 0.527818] . Log likelihood of the current tree: -45958.219621. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2623_139x1044_2006.phy_phyml_tree.txt'... . Time used 0h3m21s 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)