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

                . Sequence filename : 				 nucleic_M2916_143x897_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_M2916_143x897_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

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

. 620 sites without polymorphism (69.12%).

. Reading tree...

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

. (    1 sec) [     -3579.3114] [Branch lengths     ]
. (    3 sec) [     -3492.5165] [GTR parameters     ]
. (    3 sec) [     -3471.9822] [Alpha              ][  0.500960]
. (    4 sec) [     -3470.9251] [Branch lengths     ]
. (    5 sec) [     -3470.6691] [GTR parameters     ]
. (    6 sec) [     -3462.6506] [Alpha              ][  0.275724]
. (    6 sec) [     -3462.3391] [Branch lengths     ]
. (    8 sec) [     -3462.1317] [GTR parameters     ]
. (    8 sec) [     -3462.1272] [Alpha              ][  0.272318]
. (    8 sec) [     -3462.0544] [Branch lengths     ]
. (   10 sec) [     -3462.0515] [GTR parameters     ]
. (   10 sec) [     -3462.0515] [Alpha              ][  0.272590]
. (   10 sec) [     -3462.0378] [Branch lengths     ]
. (   11 sec) [     -3462.0373] [GTR parameters     ]
. (   11 sec) [     -3462.0373] [Alpha              ][  0.272317]
. (   12 sec) [     -3462.0355] [Branch lengths     ]
. (   12 sec) [     -3462.0354] [GTR parameters     ]
. (   13 sec) [     -3462.0354] [Alpha              ][  0.272317]
. (   13 sec) [     -3462.0350] [Branch lengths     ]
. (   14 sec) [     -3462.0350] [GTR parameters     ]
. (   14 sec) [     -3462.0350] [Alpha              ][  0.272317]
. (   14 sec) [     -3462.0350] [GTR parameters     ]
. (   14 sec) [     -3462.0350] [Alpha              ][  0.272317]
. Log likelihood of the current tree: -3462.035005.

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

. Printing the most likely tree in file 'nucleic_M2916_143x897_2006.phy_phyml_tree.txt'...


. Time used 0h0m28s

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)