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

                . Sequence filename : 				 nucleic_M2565_51x1951_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_M2565_51x1951_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 763 patterns found. (out of a total of 1951 sites) 

. 1244 sites without polymorphism (63.76%).

. Reading tree...

. This analysis requires at least 20Mo of memory space.

. (    1 sec) [    -15716.0413] [Branch lengths     ]
. (    4 sec) [    -15098.6791] [GTR parameters     ]
. (    4 sec) [    -14816.7618] [Alpha              ][  0.500960]
. (    5 sec) [    -14797.0187] [Branch lengths     ]
. (    7 sec) [    -14796.5499] [GTR parameters     ]
. (    7 sec) [    -14665.1389] [Alpha              ][  0.250961]
. (    8 sec) [    -14659.8978] [Branch lengths     ]
. (   10 sec) [    -14659.3428] [GTR parameters     ]
. (   10 sec) [    -14659.0435] [Alpha              ][  0.243184]
. (   11 sec) [    -14657.9580] [Branch lengths     ]
. (   12 sec) [    -14657.9494] [GTR parameters     ]
. (   12 sec) [    -14657.9470] [Alpha              ][  0.243843]
. (   13 sec) [    -14657.8051] [Branch lengths     ]
. (   13 sec) [    -14657.8051] [GTR parameters     ]
. (   13 sec) [    -14657.8039] [Alpha              ][  0.244278]
. (   14 sec) [    -14657.7777] [Branch lengths     ]
. (   14 sec) [    -14657.7776] [GTR parameters     ]
. (   14 sec) [    -14657.7773] [Alpha              ][  0.244522]
. (   15 sec) [    -14657.7718] [Branch lengths     ]
. (   16 sec) [    -14657.7697] [GTR parameters     ]
. (   16 sec) [    -14657.7697] [Alpha              ][  0.244522]
. (   17 sec) [    -14657.7683] [Branch lengths     ]
. (   17 sec) [    -14657.7683] [GTR parameters     ]
. (   17 sec) [    -14657.7683] [Alpha              ][  0.244522]
. (   18 sec) [    -14657.7679] [Branch lengths     ]
. (   19 sec) [    -14657.7669] [GTR parameters     ]
. (   19 sec) [    -14657.7669] [Alpha              ][  0.244522]
. (   19 sec) [    -14657.7668] [Branch lengths     ]
. (   20 sec) [    -14657.7668] [GTR parameters     ]
. (   20 sec) [    -14657.7668] [Alpha              ][  0.244767]
. (   20 sec) [    -14657.7668] [GTR parameters     ]
. (   21 sec) [    -14657.7668] [Alpha              ][  0.244767]
. Log likelihood of the current tree: -14657.766799.

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

. Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'...


. Time used 0h0m38s

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)