.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2974_56x827_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_M2974_56x827_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 330 patterns found. (out of a total of 827 sites) . 592 sites without polymorphism (71.58%). . Reading tree... . This analysis requires at least 10Mo of memory space. . ( 1 sec) [ -5902.2004] [Branch lengths ] . ( 2 sec) [ -5625.9493] [GTR parameters ] . ( 2 sec) [ -5495.3584] [Alpha ][ 0.500960] . ( 3 sec) [ -5488.6906] [Branch lengths ] . ( 4 sec) [ -5488.1942] [GTR parameters ] . ( 4 sec) [ -5401.3186] [Alpha ][ 0.250961] . ( 4 sec) [ -5400.2679] [Branch lengths ] . ( 5 sec) [ -5399.5818] [GTR parameters ] . ( 5 sec) [ -5384.6540] [Alpha ][ 0.171403] . ( 5 sec) [ -5384.3694] [Branch lengths ] . ( 6 sec) [ -5384.2419] [GTR parameters ] . ( 6 sec) [ -5384.2271] [Alpha ][ 0.169347] . ( 7 sec) [ -5384.2100] [Branch lengths ] . ( 7 sec) [ -5384.2098] [GTR parameters ] . ( 7 sec) [ -5384.2097] [Alpha ][ 0.169136] . ( 8 sec) [ -5384.2085] [Branch lengths ] . ( 8 sec) [ -5384.2085] [GTR parameters ] . ( 8 sec) [ -5384.2085] [Alpha ][ 0.169136] . ( 8 sec) [ -5384.2084] [Branch lengths ] . ( 9 sec) [ -5384.2084] [GTR parameters ] . ( 9 sec) [ -5384.2084] [Alpha ][ 0.169136] . ( 9 sec) [ -5384.2084] [GTR parameters ] . ( 9 sec) [ -5384.2084] [Alpha ][ 0.169136] . Log likelihood of the current tree: -5384.208415. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2974_56x827_2006.phy_phyml_tree.txt'... . Time used 0h0m17s 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)