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

                . Sequence filename : 				 nucleic_M2932_68x1712_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_M2932_68x1712_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 1264 patterns found. (out of a total of 1712 sites) 

. 601 sites without polymorphism (35.11%).

. Reading tree...

. This analysis requires at least 45Mo of memory space.

. (    1 sec) [    -15327.9276] [Branch lengths     ]
. (    9 sec) [    -14979.0953] [GTR parameters     ]
. (   10 sec) [    -14946.3238] [Alpha              ][  0.655947]
. (   11 sec) [    -14931.5185] [Branch lengths     ]
. (   17 sec) [    -14929.7090] [GTR parameters     ]
. (   17 sec) [    -14928.0163] [Alpha              ][  0.598894]
. (   18 sec) [    -14925.8193] [Branch lengths     ]
. (   24 sec) [    -14925.7012] [GTR parameters     ]
. (   24 sec) [    -14925.6122] [Alpha              ][  0.587026]
. (   25 sec) [    -14925.0426] [Branch lengths     ]
. (   31 sec) [    -14925.0215] [GTR parameters     ]
. (   31 sec) [    -14924.9927] [Alpha              ][  0.580092]
. (   32 sec) [    -14924.8252] [Branch lengths     ]
. (   37 sec) [    -14924.8176] [GTR parameters     ]
. (   37 sec) [    -14924.8096] [Alpha              ][  0.576453]
. (   39 sec) [    -14924.7656] [Branch lengths     ]
. (   43 sec) [    -14924.7636] [GTR parameters     ]
. (   43 sec) [    -14924.7613] [Alpha              ][  0.574479]
. (   45 sec) [    -14924.7487] [Branch lengths     ]
. (   47 sec) [    -14924.7482] [GTR parameters     ]
. (   47 sec) [    -14924.7477] [Alpha              ][  0.573532]
. (   48 sec) [    -14924.7444] [Branch lengths     ]
. (   49 sec) [    -14924.7444] [GTR parameters     ]
. (   50 sec) [    -14924.7443] [Alpha              ][  0.572959]
. (   51 sec) [    -14924.7433] [Branch lengths     ]
. (   54 sec) [    -14924.7430] [GTR parameters     ]
. (   54 sec) [    -14924.7430] [Alpha              ][  0.572959]
. (   56 sec) [    -14924.7427] [Branch lengths     ]
. (   57 sec) [    -14924.7427] [GTR parameters     ]
. (   57 sec) [    -14924.7427] [Alpha              ][  0.572959]
. (   58 sec) [    -14924.7427] [GTR parameters     ]
. (   58 sec) [    -14924.7427] [Alpha              ][  0.572959]
. Log likelihood of the current tree: -14924.742678.

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

. Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'...


. Time used 0h1m34s

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)