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

                . Sequence filename : 				 nucleic_M2662_60x1348_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_M2662_60x1348_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 664 patterns found. (out of a total of 1348 sites) 

. 794 sites without polymorphism (58.90%).

. Reading tree...

. This analysis requires at least 21Mo of memory space.

. (    1 sec) [    -13165.7764] [Branch lengths     ]
. (    6 sec) [    -12636.3017] [GTR parameters     ]
. (    6 sec) [    -12429.4484] [Alpha              ][  0.500960]
. (    7 sec) [    -12412.7626] [Branch lengths     ]
. (   10 sec) [    -12412.0563] [GTR parameters     ]
. (   10 sec) [    -12352.0207] [Alpha              ][  0.293727]
. (   11 sec) [    -12349.3135] [Branch lengths     ]
. (   13 sec) [    -12348.9152] [GTR parameters     ]
. (   13 sec) [    -12348.9150] [Alpha              ][  0.293403]
. (   14 sec) [    -12348.4959] [Branch lengths     ]
. (   14 sec) [    -12348.4915] [GTR parameters     ]
. (   14 sec) [    -12348.4897] [Alpha              ][  0.294177]
. (   15 sec) [    -12348.3835] [Branch lengths     ]
. (   16 sec) [    -12348.3828] [GTR parameters     ]
. (   16 sec) [    -12348.3821] [Alpha              ][  0.294626]
. (   16 sec) [    -12348.3579] [Branch lengths     ]
. (   17 sec) [    -12348.3578] [GTR parameters     ]
. (   17 sec) [    -12348.3578] [Alpha              ][  0.294920]
. (   18 sec) [    -12348.3515] [Branch lengths     ]
. (   18 sec) [    -12348.3512] [GTR parameters     ]
. (   18 sec) [    -12348.3512] [Alpha              ][  0.294920]
. (   19 sec) [    -12348.3496] [Branch lengths     ]
. (   19 sec) [    -12348.3496] [GTR parameters     ]
. (   19 sec) [    -12348.3496] [Alpha              ][  0.294920]
. (   20 sec) [    -12348.3492] [Branch lengths     ]
. (   20 sec) [    -12348.3492] [GTR parameters     ]
. (   20 sec) [    -12348.3492] [Alpha              ][  0.294920]
. (   21 sec) [    -12348.3492] [GTR parameters     ]
. (   21 sec) [    -12348.3492] [Alpha              ][  0.294920]
. Log likelihood of the current tree: -12348.349226.

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

. Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'...


. Time used 0h0m39s

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)