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

                . Sequence filename : 				 nucleic_M2738_53x1538_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_M2738_53x1538_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 762 patterns found. (out of a total of 1538 sites) 

. 828 sites without polymorphism (53.84%).

. Reading tree...

. This analysis requires at least 21Mo of memory space.

. (    1 sec) [    -14864.4860] [Branch lengths     ]
. (    2 sec) [    -14641.4297] [GTR parameters     ]
. (    2 sec) [    -14423.9534] [Alpha              ][  0.500960]
. (    2 sec) [    -14415.6124] [Branch lengths     ]
. (    7 sec) [    -13975.2561] [GTR parameters     ]
. (    7 sec) [    -13921.6142] [Alpha              ][  0.309610]
. (    8 sec) [    -13914.3967] [Branch lengths     ]
. (   12 sec) [    -13912.9292] [GTR parameters     ]
. (   13 sec) [    -13912.6533] [Alpha              ][  0.299638]
. (   13 sec) [    -13912.1021] [Branch lengths     ]
. (   16 sec) [    -13912.0764] [GTR parameters     ]
. (   16 sec) [    -13912.0763] [Alpha              ][  0.299338]
. (   17 sec) [    -13912.0134] [Branch lengths     ]
. (   19 sec) [    -13912.0112] [GTR parameters     ]
. (   19 sec) [    -13912.0112] [Alpha              ][  0.299338]
. (   20 sec) [    -13911.9959] [Branch lengths     ]
. (   22 sec) [    -13911.9949] [GTR parameters     ]
. (   22 sec) [    -13911.9949] [Alpha              ][  0.299338]
. (   22 sec) [    -13911.9916] [Branch lengths     ]
. (   23 sec) [    -13911.9914] [GTR parameters     ]
. (   23 sec) [    -13911.9914] [Alpha              ][  0.299338]
. (   24 sec) [    -13911.9905] [Branch lengths     ]
. (   24 sec) [    -13911.9904] [GTR parameters     ]
. (   25 sec) [    -13911.9904] [Alpha              ][  0.299338]
. (   25 sec) [    -13911.9904] [GTR parameters     ]
. (   25 sec) [    -13911.9904] [Alpha              ][  0.299338]
. Log likelihood of the current tree: -13911.990432.

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

. Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.phy_phyml_tree.txt'...


. Time used 0h0m42s

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)