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

                . Sequence filename : 				 nucleic_M2922_77x1101_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_M2922_77x1101_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 173 patterns found. (out of a total of 1101 sites) 

. 906 sites without polymorphism (82.29%).

. Reading tree...

. This analysis requires at least 7Mo of memory space.

. (    1 sec) [     -3274.3092] [Branch lengths     ]
. (    1 sec) [     -3232.7055] [GTR parameters     ]
. (    1 sec) [     -3217.5198] [Alpha              ][  0.500960]
. (    1 sec) [     -3217.2478] [Branch lengths     ]
. (    3 sec) [     -3052.5503] [GTR parameters     ]
. (    3 sec) [     -3038.4595] [Alpha              ][  0.250961]
. (    3 sec) [     -3035.4079] [Branch lengths     ]
. (    4 sec) [     -3035.0547] [GTR parameters     ]
. (    4 sec) [     -3030.0850] [Alpha              ][  0.133080]
. (    4 sec) [     -3029.7406] [Branch lengths     ]
. (    6 sec) [     -3029.6092] [GTR parameters     ]
. (    6 sec) [     -3029.6082] [Alpha              ][  0.131785]
. (    6 sec) [     -3029.5900] [Branch lengths     ]
. (    6 sec) [     -3029.5895] [GTR parameters     ]
. (    6 sec) [     -3029.5894] [Alpha              ][  0.132145]
. (    6 sec) [     -3029.5884] [Branch lengths     ]
. (    7 sec) [     -3029.5884] [GTR parameters     ]
. (    7 sec) [     -3029.5884] [Alpha              ][  0.132282]
. (    7 sec) [     -3029.5883] [Branch lengths     ]
. (    7 sec) [     -3029.5883] [GTR parameters     ]
. (    7 sec) [     -3029.5883] [Alpha              ][  0.132282]
. (    8 sec) [     -3029.5883] [GTR parameters     ]
. (    8 sec) [     -3029.5883] [Alpha              ][  0.132282]
. Log likelihood of the current tree: -3029.588305.

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

. Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'...


. Time used 0h0m14s

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)