.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2572_191x990_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_M2572_191x990_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 285 patterns found. (out of a total of 990 sites) . 729 sites without polymorphism (73.64%). . Reading tree... . This analysis requires at least 29Mo of memory space. . ( 2 sec) [ -3516.6842] [Branch lengths ] . ( 4 sec) [ -3511.9741] [GTR parameters ] . ( 4 sec) [ -3508.5033] [Alpha ][ 0.574079] . ( 5 sec) [ -3508.3692] [Branch lengths ] . ( 7 sec) [ -3508.3253] [GTR parameters ] . ( 7 sec) [ -3508.3193] [Alpha ][ 0.562384] . ( 8 sec) [ -3508.3166] [Branch lengths ] . ( 8 sec) [ -3508.3165] [GTR parameters ] . ( 9 sec) [ -3508.3165] [Alpha ][ 0.562384] . ( 9 sec) [ -3508.3164] [Branch lengths ] . ( 10 sec) [ -3508.3164] [GTR parameters ] . ( 10 sec) [ -3508.3164] [Alpha ][ 0.562384] . ( 11 sec) [ -3508.3164] [GTR parameters ] . ( 11 sec) [ -3508.3164] [Alpha ][ 0.562384] . Log likelihood of the current tree: -3508.316352. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2572_191x990_2006.phy_phyml_tree.txt'... . Time used 0h0m26s 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)