..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename : 				 nucleic_M2933_99x1634_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_M2933_99x1634_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')...

. Compressing sequences...

. 578 patterns found. (out of a total of 1634 sites) 

. 1151 sites without polymorphism (70.44%).

. Reading tree...

. This analysis requires at least 30Mo of memory space.

. (    1 sec) [     -7873.6008] [Branch lengths     ]
. (    6 sec) [     -7698.3069] [GTR parameters     ]
. (    6 sec) [     -7661.2914] [Alpha              ][  0.500960]
. (    7 sec) [     -7647.5270] [Branch lengths     ]
. (   10 sec) [     -7647.1460] [GTR parameters     ]
. (   11 sec) [     -7644.4200] [Alpha              ][  0.420446]
. (   11 sec) [     -7642.3370] [Branch lengths     ]
. (   14 sec) [     -7642.2974] [GTR parameters     ]
. (   15 sec) [     -7642.1056] [Alpha              ][  0.402010]
. (   16 sec) [     -7641.6332] [Branch lengths     ]
. (   19 sec) [     -7641.6270] [GTR parameters     ]
. (   19 sec) [     -7641.6093] [Alpha              ][  0.396459]
. (   20 sec) [     -7641.4350] [Branch lengths     ]
. (   21 sec) [     -7641.4338] [GTR parameters     ]
. (   21 sec) [     -7641.4324] [Alpha              ][  0.394899]
. (   22 sec) [     -7641.3617] [Branch lengths     ]
. (   23 sec) [     -7641.3614] [GTR parameters     ]
. (   24 sec) [     -7641.3613] [Alpha              ][  0.394327]
. (   24 sec) [     -7641.3181] [Branch lengths     ]
. (   25 sec) [     -7641.3181] [GTR parameters     ]
. (   26 sec) [     -7641.3181] [Alpha              ][  0.394327]
. (   26 sec) [     -7641.2886] [Branch lengths     ]
. (   27 sec) [     -7641.2886] [GTR parameters     ]
. (   27 sec) [     -7641.2886] [Alpha              ][  0.394327]
. (   28 sec) [     -7641.2685] [Branch lengths     ]
. (   29 sec) [     -7641.2684] [GTR parameters     ]
. (   30 sec) [     -7641.2684] [Alpha              ][  0.394327]
. (   30 sec) [     -7641.2548] [Branch lengths     ]
. (   31 sec) [     -7641.2548] [GTR parameters     ]
. (   31 sec) [     -7641.2548] [Alpha              ][  0.394327]
. (   32 sec) [     -7641.2454] [Branch lengths     ]
. (   32 sec) [     -7641.2454] [GTR parameters     ]
. (   33 sec) [     -7641.2454] [Alpha              ][  0.393932]
. (   33 sec) [     -7641.2390] [Branch lengths     ]
. (   34 sec) [     -7641.2390] [GTR parameters     ]
. (   34 sec) [     -7641.2390] [Alpha              ][  0.393932]
. (   35 sec) [     -7641.2346] [Branch lengths     ]
. (   36 sec) [     -7641.2346] [GTR parameters     ]
. (   36 sec) [     -7641.2346] [Alpha              ][  0.393932]
. (   37 sec) [     -7641.2315] [Branch lengths     ]
. (   38 sec) [     -7641.2315] [GTR parameters     ]
. (   38 sec) [     -7641.2315] [Alpha              ][  0.393932]
. (   39 sec) [     -7641.2294] [Branch lengths     ]
. (   39 sec) [     -7641.2294] [GTR parameters     ]
. (   39 sec) [     -7641.2294] [Alpha              ][  0.393932]
. (   40 sec) [     -7641.2279] [Branch lengths     ]
. (   41 sec) [     -7641.2279] [GTR parameters     ]
. (   41 sec) [     -7641.2279] [Alpha              ][  0.393932]
. (   42 sec) [     -7641.2268] [Branch lengths     ]
. (   42 sec) [     -7641.2268] [GTR parameters     ]
. (   42 sec) [     -7641.2268] [Alpha              ][  0.393932]
. (   43 sec) [     -7641.2260] [Branch lengths     ]
. (   44 sec) [     -7641.2260] [GTR parameters     ]
. (   44 sec) [     -7641.2260] [Alpha              ][  0.393932]
. (   44 sec) [     -7641.2260] [GTR parameters     ]
. (   45 sec) [     -7641.2260] [Alpha              ][  0.393932]
. Log likelihood of the current tree: -7641.226044.

. Compute aLRT branch supports on the most likely tree...

. Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'...


. Time used 0h1m7s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
java.lang.NullPointerException
	at java.io.FileInputStream.<init>(FileInputStream.java:103)
	at java.io.FileReader.<init>(FileReader.java:55)
	at Recomp.<init>(Recomp.java:114)
	at Recomp.main(Recomp.java:52)