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

                . Sequence filename : 				 nucleic_M2623_139x1044_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_M2623_139x1044_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 959 patterns found. (out of a total of 1044 sites) 

. 202 sites without polymorphism (19.35%).

. Reading tree...

. This analysis requires at least 71Mo of memory space.

. (    3 sec) [    -47873.5205] [Branch lengths     ]
. (    6 sec) [    -46742.4806] [GTR parameters     ]
. (    6 sec) [    -46462.0388] [Alpha              ][  0.587921]
. (    8 sec) [    -46416.1275] [Branch lengths     ]
. (   21 sec) [    -45906.0357] [GTR parameters     ]
. (   21 sec) [    -45898.4189] [Alpha              ][  0.534000]
. (   23 sec) [    -45880.3791] [Branch lengths     ]
. (   33 sec) [    -45878.8057] [GTR parameters     ]
. (   34 sec) [    -45878.6451] [Alpha              ][  0.526542]
. (   36 sec) [    -45872.2960] [Branch lengths     ]
. (   41 sec) [    -45872.0481] [GTR parameters     ]
. (   42 sec) [    -45872.0014] [Alpha              ][  0.530360]
. (   44 sec) [    -45868.2352] [Branch lengths     ]
. (   52 sec) [    -45868.1258] [GTR parameters     ]
. (   52 sec) [    -45868.0969] [Alpha              ][  0.533281]
. (   54 sec) [    -45866.1897] [Branch lengths     ]
. (   63 sec) [    -45866.1351] [GTR parameters     ]
. (   64 sec) [    -45866.1266] [Alpha              ][  0.534815]
. (   66 sec) [    -45865.1209] [Branch lengths     ]
. (   73 sec) [    -45865.0935] [GTR parameters     ]
. (   73 sec) [    -45865.0913] [Alpha              ][  0.535563]
. (   75 sec) [    -45864.5640] [Branch lengths     ]
. (   80 sec) [    -45864.5497] [GTR parameters     ]
. (   81 sec) [    -45864.5497] [Alpha              ][  0.535563]
. (   83 sec) [    -45864.2818] [Branch lengths     ]
. (   85 sec) [    -45864.2745] [GTR parameters     ]
. (   85 sec) [    -45864.2745] [Alpha              ][  0.535563]
. (   87 sec) [    -45864.1424] [Branch lengths     ]
. (   89 sec) [    -45864.1384] [GTR parameters     ]
. (   90 sec) [    -45864.1384] [Alpha              ][  0.535563]
. (   92 sec) [    -45864.0733] [Branch lengths     ]
. (   94 sec) [    -45864.0714] [GTR parameters     ]
. (   94 sec) [    -45864.0714] [Alpha              ][  0.535563]
. (   96 sec) [    -45864.0396] [Branch lengths     ]
. (   98 sec) [    -45864.0387] [GTR parameters     ]
. (   98 sec) [    -45864.0387] [Alpha              ][  0.535563]
. (  101 sec) [    -45864.0232] [Branch lengths     ]
. (  102 sec) [    -45864.0227] [GTR parameters     ]
. (  102 sec) [    -45864.0227] [Alpha              ][  0.535563]
. (  104 sec) [    -45864.0151] [Branch lengths     ]
. (  106 sec) [    -45864.0150] [GTR parameters     ]
. (  106 sec) [    -45864.0150] [Alpha              ][  0.535563]
. (  108 sec) [    -45864.0115] [Branch lengths     ]
. (  110 sec) [    -45864.0112] [GTR parameters     ]
. (  110 sec) [    -45864.0112] [Alpha              ][  0.535563]
. (  112 sec) [    -45864.0095] [Branch lengths     ]
. (  114 sec) [    -45864.0092] [GTR parameters     ]
. (  114 sec) [    -45864.0092] [Alpha              ][  0.535563]
. (  116 sec) [    -45864.0082] [Branch lengths     ]
. (  118 sec) [    -45864.0082] [GTR parameters     ]
. (  118 sec) [    -45864.0082] [Alpha              ][  0.535563]
. (  120 sec) [    -45864.0076] [Branch lengths     ]
. (  121 sec) [    -45864.0076] [GTR parameters     ]
. (  122 sec) [    -45864.0076] [Alpha              ][  0.535563]
. (  123 sec) [    -45864.0076] [GTR parameters     ]
. (  123 sec) [    -45864.0076] [Alpha              ][  0.535563]
. Log likelihood of the current tree: -45864.007642.

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

. Printing the most likely tree in file 'nucleic_M2623_139x1044_2006.phy_phyml_tree.txt'...


. Time used 0h3m3s

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)