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

                . Sequence filename : 				 nucleic_M2655_50x872_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_M2655_50x872_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 374 patterns found. (out of a total of 872 sites) 

. 550 sites without polymorphism (63.07%).

. Reading tree...

. This analysis requires at least 10Mo of memory space.

. (    0 sec) [     -7072.6817] [Branch lengths     ]
. (    1 sec) [     -6712.0120] [GTR parameters     ]
. (    1 sec) [     -6589.4539] [Alpha              ][  0.500960]
. (    2 sec) [     -6582.3364] [Branch lengths     ]
. (    3 sec) [     -6581.5888] [GTR parameters     ]
. (    3 sec) [     -6524.8867] [Alpha              ][  0.250961]
. (    3 sec) [     -6523.4250] [Branch lengths     ]
. (    4 sec) [     -6522.5824] [GTR parameters     ]
. (    4 sec) [     -6522.1264] [Alpha              ][  0.236070]
. (    5 sec) [     -6521.7012] [Branch lengths     ]
. (    5 sec) [     -6521.6869] [GTR parameters     ]
. (    5 sec) [     -6521.6869] [Alpha              ][  0.235834]
. (    6 sec) [     -6521.4878] [Branch lengths     ]
. (    6 sec) [     -6521.4868] [GTR parameters     ]
. (    6 sec) [     -6521.4867] [Alpha              ][  0.236070]
. (    6 sec) [     -6521.4739] [Branch lengths     ]
. (    6 sec) [     -6521.4738] [GTR parameters     ]
. (    7 sec) [     -6521.4738] [Alpha              ][  0.236070]
. (    7 sec) [     -6521.4732] [Branch lengths     ]
. (    7 sec) [     -6521.4732] [GTR parameters     ]
. (    7 sec) [     -6521.4732] [Alpha              ][  0.236070]
. (    7 sec) [     -6521.4732] [GTR parameters     ]
. (    7 sec) [     -6521.4732] [Alpha              ][  0.236070]
. Log likelihood of the current tree: -6521.473170.

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

. Printing the most likely tree in file 'nucleic_M2655_50x872_2006.phy_phyml_tree.txt'...


. Time used 0h0m15s

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)