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

                . Sequence filename : 				 nucleic_M2933_99x1634_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 (RAxML_result.nucleic_M2933_99x1634_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 578 patterns found. (out of a total of 1634 sites) 

. 1151 sites without polymorphism (70.44%).

. Reading tree...

. This analysis requires at least 30Mo of memory space.

. (    1 sec) [     -7850.2174] [Branch lengths     ]
. (    6 sec) [     -7667.3047] [GTR parameters     ]
. (    6 sec) [     -7630.3462] [Alpha              ][  0.500960]
. (    7 sec) [     -7621.9580] [Branch lengths     ]
. (   10 sec) [     -7621.6532] [GTR parameters     ]
. (   10 sec) [     -7619.5720] [Alpha              ][  0.429138]
. (   11 sec) [     -7618.5535] [Branch lengths     ]
. (   14 sec) [     -7618.5328] [GTR parameters     ]
. (   14 sec) [     -7618.3791] [Alpha              ][  0.411928]
. (   15 sec) [     -7618.1981] [Branch lengths     ]
. (   17 sec) [     -7618.1963] [GTR parameters     ]
. (   17 sec) [     -7618.1807] [Alpha              ][  0.406470]
. (   18 sec) [     -7618.1489] [Branch lengths     ]
. (   20 sec) [     -7618.1486] [GTR parameters     ]
. (   20 sec) [     -7618.1474] [Alpha              ][  0.404925]
. (   21 sec) [     -7618.1423] [Branch lengths     ]
. (   22 sec) [     -7618.1423] [GTR parameters     ]
. (   22 sec) [     -7618.1421] [Alpha              ][  0.404352]
. (   23 sec) [     -7618.1412] [Branch lengths     ]
. (   24 sec) [     -7618.1412] [GTR parameters     ]
. (   24 sec) [     -7618.1412] [Alpha              ][  0.404352]
. (   24 sec) [     -7618.1412] [GTR parameters     ]
. (   25 sec) [     -7618.1412] [Alpha              ][  0.404352]
. Log likelihood of the current tree: -7618.141180.

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

. Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'...


. Time used 0h0m47s

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)