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

                . Sequence filename : 				 nucleic_M2946_110x1003_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_M2946_110x1003_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...

. 614 patterns found. (out of a total of 1003 sites) 

. 462 sites without polymorphism (46.06%).

. Reading tree...

. This analysis requires at least 36Mo of memory space.

. (    1 sec) [    -18430.5491] [Branch lengths     ]
. (    8 sec) [    -17404.3895] [GTR parameters     ]
. (    8 sec) [    -17152.5443] [Alpha              ][  0.500960]
. (    9 sec) [    -17115.9128] [Branch lengths     ]
. (   13 sec) [    -17112.6481] [GTR parameters     ]
. (   13 sec) [    -17078.4865] [Alpha              ][  0.358636]
. (   14 sec) [    -17070.1801] [Branch lengths     ]
. (   17 sec) [    -17069.2604] [GTR parameters     ]
. (   18 sec) [    -17069.2600] [Alpha              ][  0.358995]
. (   19 sec) [    -17066.2481] [Branch lengths     ]
. (   22 sec) [    -17066.1875] [GTR parameters     ]
. (   22 sec) [    -17066.1801] [Alpha              ][  0.360664]
. (   23 sec) [    -17064.9262] [Branch lengths     ]
. (   26 sec) [    -17064.9078] [GTR parameters     ]
. (   26 sec) [    -17064.9047] [Alpha              ][  0.361730]
. (   27 sec) [    -17064.3919] [Branch lengths     ]
. (   30 sec) [    -17064.3832] [GTR parameters     ]
. (   30 sec) [    -17064.3825] [Alpha              ][  0.362208]
. (   31 sec) [    -17064.1717] [Branch lengths     ]
. (   32 sec) [    -17064.1684] [GTR parameters     ]
. (   32 sec) [    -17064.1682] [Alpha              ][  0.362570]
. (   34 sec) [    -17064.0855] [Branch lengths     ]
. (   34 sec) [    -17064.0842] [GTR parameters     ]
. (   34 sec) [    -17064.0842] [Alpha              ][  0.362570]
. (   36 sec) [    -17064.0514] [Branch lengths     ]
. (   36 sec) [    -17064.0509] [GTR parameters     ]
. (   36 sec) [    -17064.0509] [Alpha              ][  0.362570]
. (   38 sec) [    -17064.0386] [Branch lengths     ]
. (   38 sec) [    -17064.0382] [GTR parameters     ]
. (   39 sec) [    -17064.0381] [Alpha              ][  0.362932]
. (   40 sec) [    -17064.0332] [Branch lengths     ]
. (   40 sec) [    -17064.0331] [GTR parameters     ]
. (   41 sec) [    -17064.0331] [Alpha              ][  0.362932]
. (   42 sec) [    -17064.0311] [Branch lengths     ]
. (   42 sec) [    -17064.0311] [GTR parameters     ]
. (   42 sec) [    -17064.0311] [Alpha              ][  0.362932]
. (   43 sec) [    -17064.0303] [Branch lengths     ]
. (   44 sec) [    -17064.0303] [GTR parameters     ]
. (   44 sec) [    -17064.0303] [Alpha              ][  0.362932]
. (   45 sec) [    -17064.0303] [GTR parameters     ]
. (   45 sec) [    -17064.0303] [Alpha              ][  0.362932]
. Log likelihood of the current tree: -17064.030302.

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

. Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'...


. Time used 0h1m14s

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)