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

                . Sequence filename : 				 nucleic_M2845_68x1715_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_M2845_68x1715_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...

. 649 patterns found. (out of a total of 1715 sites) 

. 1119 sites without polymorphism (65.25%).

. Reading tree...

. This analysis requires at least 23Mo of memory space.

. (    1 sec) [    -11959.0673] [Branch lengths     ]
. (    5 sec) [    -11623.7244] [GTR parameters     ]
. (    5 sec) [    -11456.9628] [Alpha              ][  0.500960]
. (    6 sec) [    -11444.3357] [Branch lengths     ]
. (    9 sec) [    -11444.1564] [GTR parameters     ]
. (    9 sec) [    -11369.0303] [Alpha              ][  0.253303]
. (   10 sec) [    -11363.7937] [Branch lengths     ]
. (   11 sec) [    -11363.5872] [GTR parameters     ]
. (   11 sec) [    -11363.5862] [Alpha              ][  0.253838]
. (   12 sec) [    -11361.9592] [Branch lengths     ]
. (   14 sec) [    -11361.9561] [GTR parameters     ]
. (   15 sec) [    -11361.9558] [Alpha              ][  0.254130]
. (   15 sec) [    -11361.4665] [Branch lengths     ]
. (   17 sec) [    -11361.4649] [GTR parameters     ]
. (   17 sec) [    -11361.4649] [Alpha              ][  0.254130]
. (   18 sec) [    -11361.3085] [Branch lengths     ]
. (   18 sec) [    -11361.3084] [GTR parameters     ]
. (   19 sec) [    -11361.3084] [Alpha              ][  0.254130]
. (   19 sec) [    -11361.2604] [Branch lengths     ]
. (   20 sec) [    -11361.2597] [GTR parameters     ]
. (   21 sec) [    -11361.2597] [Alpha              ][  0.254130]
. (   21 sec) [    -11361.2439] [Branch lengths     ]
. (   22 sec) [    -11361.2439] [GTR parameters     ]
. (   22 sec) [    -11361.2439] [Alpha              ][  0.254130]
. (   23 sec) [    -11361.2389] [Branch lengths     ]
. (   24 sec) [    -11361.2385] [GTR parameters     ]
. (   24 sec) [    -11361.2385] [Alpha              ][  0.254130]
. (   25 sec) [    -11361.2368] [Branch lengths     ]
. (   25 sec) [    -11361.2368] [GTR parameters     ]
. (   25 sec) [    -11361.2368] [Alpha              ][  0.254130]
. (   26 sec) [    -11361.2362] [Branch lengths     ]
. (   26 sec) [    -11361.2362] [GTR parameters     ]
. (   26 sec) [    -11361.2362] [Alpha              ][  0.254130]
. (   27 sec) [    -11361.2362] [GTR parameters     ]
. (   27 sec) [    -11361.2362] [Alpha              ][  0.254130]
. Log likelihood of the current tree: -11361.236191.

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

. Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'...


. Time used 0h0m49s

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)