.......................... 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 (RAxML_result.nucleic_M2707_115x1677_2006.phy_RAXML_CAT)" . 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) [ -10378.6208] [Branch lengths ] . ( 10 sec) [ -10191.8824] [GTR parameters ] . ( 10 sec) [ -9907.5045] [Alpha ][ 0.500960] . ( 12 sec) [ -9876.8223] [Branch lengths ] . ( 17 sec) [ -9875.9475] [GTR parameters ] . ( 18 sec) [ -9794.6525] [Alpha ][ 0.264760] . ( 19 sec) [ -9779.2309] [Branch lengths ] . ( 25 sec) [ -9777.2687] [GTR parameters ] . ( 26 sec) [ -9776.4817] [Alpha ][ 0.250106] . ( 27 sec) [ -9764.1130] [Branch lengths ] . ( 34 sec) [ -9763.7046] [GTR parameters ] . ( 34 sec) [ -9763.2540] [Alpha ][ 0.240038] . ( 35 sec) [ -9751.4908] [Branch lengths ] . ( 39 sec) [ -9751.3377] [GTR parameters ] . ( 40 sec) [ -9750.5386] [Alpha ][ 0.227692] . ( 41 sec) [ -9742.9889] [Branch lengths ] . ( 44 sec) [ -9742.8671] [GTR parameters ] . ( 44 sec) [ -9742.0621] [Alpha ][ 0.216028] . ( 45 sec) [ -9737.8274] [Branch lengths ] . ( 50 sec) [ -9737.7385] [GTR parameters ] . ( 50 sec) [ -9737.2835] [Alpha ][ 0.207614] . ( 52 sec) [ -9734.9636] [Branch lengths ] . ( 54 sec) [ -9734.9104] [GTR parameters ] . ( 55 sec) [ -9734.7011] [Alpha ][ 0.202089] . ( 56 sec) [ -9733.0580] [Branch lengths ] . ( 61 sec) [ -9733.0222] [GTR parameters ] . ( 61 sec) [ -9732.8928] [Alpha ][ 0.197871] . ( 62 sec) [ -9731.5202] [Branch lengths ] . ( 67 sec) [ -9731.4897] [GTR parameters ] . ( 67 sec) [ -9731.3899] [Alpha ][ 0.194253] . ( 69 sec) [ -9730.3664] [Branch lengths ] . ( 73 sec) [ -9730.3442] [GTR parameters ] . ( 73 sec) [ -9730.2523] [Alpha ][ 0.190844] . ( 74 sec) [ -9729.5731] [Branch lengths ] . ( 78 sec) [ -9729.5595] [GTR parameters ] . ( 79 sec) [ -9729.4843] [Alpha ][ 0.187809] . ( 80 sec) [ -9729.0807] [Branch lengths ] . ( 84 sec) [ -9729.0715] [GTR parameters ] . ( 85 sec) [ -9729.0194] [Alpha ][ 0.185328] . ( 86 sec) [ -9728.7898] [Branch lengths ] . ( 87 sec) [ -9728.7850] [GTR parameters ] . ( 87 sec) [ -9728.7524] [Alpha ][ 0.183401] . ( 89 sec) [ -9728.6267] [Branch lengths ] . ( 90 sec) [ -9728.6238] [GTR parameters ] . ( 90 sec) [ -9728.6048] [Alpha ][ 0.181785] . ( 91 sec) [ -9728.5324] [Branch lengths ] . ( 93 sec) [ -9728.5307] [GTR parameters ] . ( 93 sec) [ -9728.5222] [Alpha ][ 0.180694] . ( 94 sec) [ -9728.4824] [Branch lengths ] . ( 95 sec) [ -9728.4815] [GTR parameters ] . ( 96 sec) [ -9728.4771] [Alpha ][ 0.179896] . ( 97 sec) [ -9728.4549] [Branch lengths ] . ( 98 sec) [ -9728.4545] [GTR parameters ] . ( 98 sec) [ -9728.4522] [Alpha ][ 0.179313] . ( 99 sec) [ -9728.4396] [Branch lengths ] . ( 101 sec) [ -9728.4393] [GTR parameters ] . ( 101 sec) [ -9728.4381] [Alpha ][ 0.178884] . ( 102 sec) [ -9728.4305] [Branch lengths ] . ( 103 sec) [ -9728.4304] [GTR parameters ] . ( 104 sec) [ -9728.4298] [Alpha ][ 0.178572] . ( 105 sec) [ -9728.4250] [Branch lengths ] . ( 106 sec) [ -9728.4249] [GTR parameters ] . ( 106 sec) [ -9728.4247] [Alpha ][ 0.178349] . ( 107 sec) [ -9728.4214] [Branch lengths ] . ( 108 sec) [ -9728.4212] [GTR parameters ] . ( 108 sec) [ -9728.4211] [Alpha ][ 0.178171] . ( 110 sec) [ -9728.4185] [Branch lengths ] . ( 110 sec) [ -9728.4185] [GTR parameters ] . ( 111 sec) [ -9728.4185] [Alpha ][ 0.178171] . ( 112 sec) [ -9728.4166] [Branch lengths ] . ( 113 sec) [ -9728.4166] [GTR parameters ] . ( 113 sec) [ -9728.4165] [Alpha ][ 0.177989] . ( 114 sec) [ -9728.4161] [Branch lengths ] . ( 115 sec) [ -9728.4161] [GTR parameters ] . ( 116 sec) [ -9728.4161] [Alpha ][ 0.177989] . ( 117 sec) [ -9728.4161] [GTR parameters ] . ( 117 sec) [ -9728.4161] [Alpha ][ 0.177989] . Log likelihood of the current tree: -9728.416054. . 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 0h2m28s 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)