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

                . Sequence filename : 				 nucleic_M2711_123x1181_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_M2711_123x1181_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 617 patterns found. (out of a total of 1181 sites) 

. 633 sites without polymorphism (53.60%).

. Reading tree...

. This analysis requires at least 40Mo of memory space.

. (    2 sec) [    -11262.3416] [Branch lengths     ]
. (   10 sec) [    -10948.7811] [GTR parameters     ]
. (   11 sec) [    -10758.5403] [Alpha              ][  0.500960]
. (   12 sec) [    -10744.3951] [Branch lengths     ]
. (   18 sec) [    -10743.0266] [GTR parameters     ]
. (   19 sec) [    -10682.3640] [Alpha              ][  0.282880]
. (   20 sec) [    -10677.2770] [Branch lengths     ]
. (   25 sec) [    -10676.1411] [GTR parameters     ]
. (   26 sec) [    -10675.9771] [Alpha              ][  0.275209]
. (   27 sec) [    -10675.0916] [Branch lengths     ]
. (   32 sec) [    -10675.0673] [GTR parameters     ]
. (   32 sec) [    -10675.0673] [Alpha              ][  0.275209]
. (   33 sec) [    -10674.8572] [Branch lengths     ]
. (   37 sec) [    -10674.8554] [GTR parameters     ]
. (   37 sec) [    -10674.8554] [Alpha              ][  0.275209]
. (   38 sec) [    -10674.8011] [Branch lengths     ]
. (   41 sec) [    -10674.8008] [GTR parameters     ]
. (   41 sec) [    -10674.8008] [Alpha              ][  0.275209]
. (   42 sec) [    -10674.7850] [Branch lengths     ]
. (   43 sec) [    -10674.7850] [GTR parameters     ]
. (   44 sec) [    -10674.7850] [Alpha              ][  0.275209]
. (   45 sec) [    -10674.7794] [Branch lengths     ]
. (   45 sec) [    -10674.7794] [GTR parameters     ]
. (   46 sec) [    -10674.7794] [Alpha              ][  0.275209]
. (   47 sec) [    -10674.7778] [Branch lengths     ]
. (   48 sec) [    -10674.7777] [GTR parameters     ]
. (   48 sec) [    -10674.7777] [Alpha              ][  0.275209]
. (   49 sec) [    -10674.7773] [Branch lengths     ]
. (   49 sec) [    -10674.7773] [GTR parameters     ]
. (   50 sec) [    -10674.7773] [Alpha              ][  0.275209]
. (   51 sec) [    -10674.7773] [GTR parameters     ]
. (   51 sec) [    -10674.7773] [Alpha              ][  0.275209]
. Log likelihood of the current tree: -10674.777339.

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

. Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'...


. Time used 0h1m19s

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)