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

                . Sequence filename : 				 nucleic_M2928_81x1651_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_M2928_81x1651_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 507 patterns found. (out of a total of 1651 sites) 

. 1189 sites without polymorphism (72.02%).

. Reading tree...

. This analysis requires at least 22Mo of memory space.

. (    1 sec) [     -7479.6706] [Branch lengths     ]
. (    2 sec) [     -7214.5809] [GTR parameters     ]
. (    2 sec) [     -7153.6585] [Alpha              ][  0.500960]
. (    3 sec) [     -7153.4305] [Branch lengths     ]
. (    4 sec) [     -6781.0165] [GTR parameters     ]
. (    4 sec) [     -6744.9849] [Alpha              ][  0.250961]
. (    5 sec) [     -6743.0054] [Branch lengths     ]
. (    9 sec) [     -6695.9878] [GTR parameters     ]
. (    9 sec) [     -6693.3952] [Alpha              ][  0.204651]
. (    9 sec) [     -6692.1022] [Branch lengths     ]
. (   13 sec) [     -6691.9619] [GTR parameters     ]
. (   13 sec) [     -6691.9616] [Alpha              ][  0.204227]
. (   13 sec) [     -6691.7932] [Branch lengths     ]
. (   16 sec) [     -6691.7918] [GTR parameters     ]
. (   16 sec) [     -6691.7897] [Alpha              ][  0.205386]
. (   16 sec) [     -6691.7712] [Branch lengths     ]
. (   17 sec) [     -6691.7712] [GTR parameters     ]
. (   17 sec) [     -6691.7710] [Alpha              ][  0.205757]
. (   17 sec) [     -6691.7691] [Branch lengths     ]
. (   20 sec) [     -6691.7682] [GTR parameters     ]
. (   20 sec) [     -6691.7682] [Alpha              ][  0.205757]
. (   20 sec) [     -6691.7679] [Branch lengths     ]
. (   21 sec) [     -6691.7678] [GTR parameters     ]
. (   21 sec) [     -6691.7678] [Alpha              ][  0.205757]
. (   21 sec) [     -6691.7678] [GTR parameters     ]
. (   22 sec) [     -6691.7678] [Alpha              ][  0.205757]
. Log likelihood of the current tree: -6691.767807.

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

. Printing the most likely tree in file 'nucleic_M2928_81x1651_2006.phy_phyml_tree.txt'...


. Time used 0h0m35s

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)