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

                . Sequence filename : 				 nucleic_M2913_81x897_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_M2913_81x897_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 197 patterns found. (out of a total of 897 sites) 

. 676 sites without polymorphism (75.36%).

. Reading tree...

. This analysis requires at least 8Mo of memory space.

. (    0 sec) [     -2510.1587] [Branch lengths     ]
. (    1 sec) [     -2455.9178] [GTR parameters     ]
. (    1 sec) [     -2442.2400] [Alpha              ][  0.500960]
. (    1 sec) [     -2441.8081] [Branch lengths     ]
. (    2 sec) [     -2441.7652] [GTR parameters     ]
. (    2 sec) [     -2431.4017] [Alpha              ][  0.250961]
. (    2 sec) [     -2431.1699] [Branch lengths     ]
. (    2 sec) [     -2431.1233] [GTR parameters     ]
. (    2 sec) [     -2428.1936] [Alpha              ][  0.136775]
. (    3 sec) [     -2428.1423] [Branch lengths     ]
. (    3 sec) [     -2428.1186] [GTR parameters     ]
. (    3 sec) [     -2428.1158] [Alpha              ][  0.133814]
. (    3 sec) [     -2428.1142] [Branch lengths     ]
. (    3 sec) [     -2428.1142] [GTR parameters     ]
. (    3 sec) [     -2428.1142] [Alpha              ][  0.133680]
. (    4 sec) [     -2428.1138] [Branch lengths     ]
. (    4 sec) [     -2428.1138] [GTR parameters     ]
. (    4 sec) [     -2428.1138] [Alpha              ][  0.133680]
. (    4 sec) [     -2428.1138] [GTR parameters     ]
. (    4 sec) [     -2428.1138] [Alpha              ][  0.133680]
. Log likelihood of the current tree: -2428.113767.

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

. Printing the most likely tree in file 'nucleic_M2913_81x897_2006.phy_phyml_tree.txt'...


. Time used 0h0m9s

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)