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

                . Sequence filename : 				 nucleic_M2771_52x1896_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_M2771_52x1896_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 906 patterns found. (out of a total of 1896 sites) 

. 1193 sites without polymorphism (62.92%).

. Reading tree...

. This analysis requires at least 24Mo of memory space.

. (    1 sec) [    -15248.3975] [Branch lengths     ]
. (    2 sec) [    -14835.0657] [GTR parameters     ]
. (    2 sec) [    -14596.9862] [Alpha              ][  0.500960]
. (    3 sec) [    -14595.3967] [Branch lengths     ]
. (    8 sec) [    -14101.2058] [GTR parameters     ]
. (    8 sec) [    -13993.0934] [Alpha              ][  0.250961]
. (    9 sec) [    -13988.6165] [Branch lengths     ]
. (   14 sec) [    -13987.7457] [GTR parameters     ]
. (   14 sec) [    -13987.7215] [Alpha              ][  0.248427]
. (   15 sec) [    -13987.0029] [Branch lengths     ]
. (   17 sec) [    -13986.9948] [GTR parameters     ]
. (   17 sec) [    -13986.9878] [Alpha              ][  0.249719]
. (   18 sec) [    -13986.4285] [Branch lengths     ]
. (   21 sec) [    -13986.4262] [GTR parameters     ]
. (   21 sec) [    -13986.4250] [Alpha              ][  0.250216]
. (   22 sec) [    -13986.1046] [Branch lengths     ]
. (   24 sec) [    -13986.1037] [GTR parameters     ]
. (   24 sec) [    -13986.1035] [Alpha              ][  0.250466]
. (   25 sec) [    -13986.0984] [Branch lengths     ]
. (   27 sec) [    -13986.0983] [GTR parameters     ]
. (   27 sec) [    -13986.0983] [Alpha              ][  0.250466]
. (   28 sec) [    -13986.0974] [Branch lengths     ]
. (   29 sec) [    -13986.0973] [GTR parameters     ]
. (   29 sec) [    -13986.0973] [Alpha              ][  0.250717]
. (   30 sec) [    -13986.0970] [Branch lengths     ]
. (   31 sec) [    -13986.0970] [GTR parameters     ]
. (   31 sec) [    -13986.0970] [Alpha              ][  0.250717]
. (   33 sec) [    -13986.0969] [GTR parameters     ]
. (   33 sec) [    -13986.0969] [Alpha              ][  0.250717]
. Log likelihood of the current tree: -13986.096944.

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

. Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'...


. Time used 0h0m53s

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)