.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2922_77x1101_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_M2922_77x1101_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 173 patterns found. (out of a total of 1101 sites) . 906 sites without polymorphism (82.29%). . Reading tree... . This analysis requires at least 7Mo of memory space. . ( 1 sec) [ -3268.5374] [Branch lengths ] . ( 1 sec) [ -3229.0097] [GTR parameters ] . ( 1 sec) [ -3216.6266] [Alpha ][ 0.500960] . ( 1 sec) [ -3216.4445] [Branch lengths ] . ( 2 sec) [ -3060.6307] [GTR parameters ] . ( 3 sec) [ -3048.7160] [Alpha ][ 0.250961] . ( 3 sec) [ -3045.2579] [Branch lengths ] . ( 4 sec) [ -3044.9137] [GTR parameters ] . ( 4 sec) [ -3040.9738] [Alpha ][ 0.138887] . ( 4 sec) [ -3040.5259] [Branch lengths ] . ( 6 sec) [ -3040.3869] [GTR parameters ] . ( 6 sec) [ -3040.3843] [Alpha ][ 0.136729] . ( 6 sec) [ -3040.3335] [Branch lengths ] . ( 6 sec) [ -3040.3320] [GTR parameters ] . ( 6 sec) [ -3040.3319] [Alpha ][ 0.137132] . ( 7 sec) [ -3040.3269] [Branch lengths ] . ( 7 sec) [ -3040.3269] [GTR parameters ] . ( 7 sec) [ -3040.3269] [Alpha ][ 0.137352] . ( 7 sec) [ -3040.3264] [Branch lengths ] . ( 7 sec) [ -3040.3263] [GTR parameters ] . ( 7 sec) [ -3040.3263] [Alpha ][ 0.137352] . ( 7 sec) [ -3040.3263] [GTR parameters ] . ( 7 sec) [ -3040.3263] [Alpha ][ 0.137352] . Log likelihood of the current tree: -3040.326349. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Time used 0h0m13s 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)