.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_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_M2588_68x1196_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . Reading tree... . This analysis requires at least 26Mo of memory space. . ( 1 sec) [ -12874.6063] [Branch lengths ] . ( 8 sec) [ -12291.2481] [GTR parameters ] . ( 8 sec) [ -12115.2719] [Alpha ][ 0.500960] . ( 9 sec) [ -12091.0647] [Branch lengths ] . ( 14 sec) [ -12085.9889] [GTR parameters ] . ( 14 sec) [ -12045.0477] [Alpha ][ 0.322629] . ( 15 sec) [ -12036.9861] [Branch lengths ] . ( 19 sec) [ -12034.3456] [GTR parameters ] . ( 19 sec) [ -12033.6433] [Alpha ][ 0.305569] . ( 20 sec) [ -12031.1848] [Branch lengths ] . ( 24 sec) [ -12030.8354] [GTR parameters ] . ( 24 sec) [ -12030.8195] [Alpha ][ 0.303005] . ( 25 sec) [ -12029.8438] [Branch lengths ] . ( 31 sec) [ -12029.7723] [GTR parameters ] . ( 31 sec) [ -12029.7719] [Alpha ][ 0.302550] . ( 32 sec) [ -12029.3802] [Branch lengths ] . ( 35 sec) [ -12029.3598] [GTR parameters ] . ( 35 sec) [ -12029.3597] [Alpha ][ 0.302247] . ( 36 sec) [ -12029.2028] [Branch lengths ] . ( 40 sec) [ -12029.1965] [GTR parameters ] . ( 40 sec) [ -12029.1965] [Alpha ][ 0.302247] . ( 40 sec) [ -12029.1296] [Branch lengths ] . ( 44 sec) [ -12029.1272] [GTR parameters ] . ( 44 sec) [ -12029.1272] [Alpha ][ 0.302247] . ( 45 sec) [ -12029.0937] [Branch lengths ] . ( 47 sec) [ -12029.0931] [GTR parameters ] . ( 47 sec) [ -12029.0931] [Alpha ][ 0.302247] . ( 47 sec) [ -12029.0767] [Branch lengths ] . ( 51 sec) [ -12029.0753] [GTR parameters ] . ( 51 sec) [ -12029.0753] [Alpha ][ 0.302247] . ( 52 sec) [ -12029.0681] [Branch lengths ] . ( 54 sec) [ -12029.0680] [GTR parameters ] . ( 54 sec) [ -12029.0680] [Alpha ][ 0.302247] . ( 55 sec) [ -12029.0644] [Branch lengths ] . ( 57 sec) [ -12029.0644] [GTR parameters ] . ( 57 sec) [ -12029.0644] [Alpha ][ 0.302247] . ( 58 sec) [ -12029.0625] [Branch lengths ] . ( 59 sec) [ -12029.0625] [GTR parameters ] . ( 59 sec) [ -12029.0625] [Alpha ][ 0.302247] . ( 59 sec) [ -12029.0615] [Branch lengths ] . ( 61 sec) [ -12029.0615] [GTR parameters ] . ( 61 sec) [ -12029.0615] [Alpha ][ 0.302247] . ( 61 sec) [ -12029.0609] [Branch lengths ] . ( 63 sec) [ -12029.0609] [GTR parameters ] . ( 63 sec) [ -12029.0609] [Alpha ][ 0.302247] . ( 64 sec) [ -12029.0609] [GTR parameters ] . ( 64 sec) [ -12029.0609] [Alpha ][ 0.302247] . Log likelihood of the current tree: -12029.060878. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 0h1m22s 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)