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

                . Sequence filename : 				 smart-gap-naked_convert.phy
                . Data type :             			 aa
                . Sequence format : 				 interleaved
                . Number of data sets : 			 1
                . Nb of bootstrapped data sets : 		 0
                . Compute approximate likelihood ratio test : 	 yes (Minimum of SH-like and Chi2-based branch supports)
                . Model name : 					 C20
                . Proportion of invariable sites :		 estimated
                . Number of subst. rate categs : 		 5
                . Gamma distribution parameter : 		 estimated
                . Amino acid equilibrium frequencies : 		 empirical
                . Optimise tree topology : 			 yes
                . Tree topology search : 			 SPRs
                . Random input tree : 				 no
                . Starting tree : 				 BIONJ
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo


nM = 0 nK = 5

. Compressing sequences...
Coming here: BuildCategory
Error: 

. 27506 patterns found. (out of a total of 27506 sites) 

. 5314 sites without polymorphism (19.32%).
C20
0.086241 0.017194 0.079129 0.032991 0.013050 0.016905 0.018453 0.036691 0.010801 0.009791 0.011283 0.022020 0.008782 0.004416 0.018927 0.317815 0.271170 0.001532 0.004834 0.017975 

Rate = 80.660607
Real rate = 0.806606
0.203558 0.005098 0.007705 0.003166 0.034867 0.006404 0.007086 0.019524 0.002439 0.115257 0.078978 0.004238 0.030919 0.011243 0.016419 0.049678 0.111895 0.001776 0.004845 0.284906 

Rate = 83.969673
Real rate = 0.839697
0.021155 0.001495 0.001276 0.000549 0.004819 0.001233 0.001454 0.001143 0.001135 0.392846 0.125064 0.001358 0.020979 0.012825 0.002025 0.002624 0.017191 0.001159 0.003603 0.386068 

Rate = 67.957410
Real rate = 0.679574
0.037690 0.288520 0.036541 0.010947 0.006407 0.089356 0.035837 0.019111 0.032951 0.010171 0.023750 0.289763 0.009653 0.003635 0.010534 0.035631 0.035593 0.002793 0.006656 0.014462 

Rate = 81.547493
Real rate = 0.815475
0.008460 0.005359 0.007253 0.002449 0.008491 0.004278 0.002506 0.002428 0.043321 0.009771 0.038051 0.002674 0.008072 0.342046 0.002142 0.008042 0.005532 0.049484 0.437500 0.012141 

Rate = 68.514810
Real rate = 0.685148
0.175990 0.029043 0.033285 0.130126 0.001756 0.070718 0.218217 0.040954 0.013071 0.008562 0.015953 0.054295 0.005405 0.002528 0.037102 0.079348 0.054008 0.001059 0.003626 0.024955 

Rate = 88.113468
Real rate = 0.881135
0.163440 0.019554 0.043870 0.037427 0.008866 0.013755 0.022061 0.529672 0.009001 0.001757 0.006116 0.016712 0.002939 0.003064 0.012646 0.082934 0.014284 0.002864 0.003240 0.005799 

Rate = 68.055983
Real rate = 0.680560
0.091747 0.026585 0.029070 0.013382 0.028402 0.025508 0.019688 0.024990 0.044977 0.058356 0.115501 0.016492 0.039599 0.099848 0.020992 0.073648 0.066152 0.024646 0.097233 0.083186 

Rate = 92.958146
Real rate = 0.929581
0.064670 0.098802 0.022891 0.016873 0.007712 0.099641 0.054498 0.014889 0.031385 0.050598 0.184428 0.090793 0.077484 0.021915 0.010500 0.032120 0.041177 0.008430 0.020611 0.050582 

Rate = 91.388940
Real rate = 0.913889
0.013599 0.004341 0.001847 0.000795 0.010009 0.004642 0.001801 0.002679 0.007240 0.081403 0.366142 0.002516 0.073497 0.264097 0.003899 0.004367 0.007525 0.026156 0.066097 0.057347 

Rate = 77.533344
Real rate = 0.775333
0.147804 0.084285 0.072663 0.053474 0.004883 0.075717 0.072725 0.090773 0.026229 0.003578 0.012678 0.105166 0.005962 0.002990 0.015656 0.145990 0.063488 0.001593 0.005076 0.009272 

Rate = 90.595630
Real rate = 0.905956
0.018638 0.004206 0.001987 0.000833 0.005497 0.006589 0.002025 0.002171 0.002367 0.202081 0.437038 0.002912 0.124186 0.038538 0.004067 0.004618 0.014990 0.002687 0.005632 0.118938 

Rate = 73.633954
Real rate = 0.736340
0.047762 0.050574 0.020957 0.014135 0.007579 0.042930 0.046269 0.005233 0.016535 0.174150 0.112125 0.057758 0.033029 0.013069 0.012437 0.026499 0.095175 0.003166 0.011247 0.209370 

Rate = 88.879442
Real rate = 0.888794
0.416419 0.005610 0.009170 0.004513 0.040694 0.006132 0.006323 0.094619 0.003106 0.007644 0.009989 0.003894 0.006932 0.004844 0.018784 0.236077 0.074627 0.001217 0.003483 0.045923 

Rate = 75.174139
Real rate = 0.751741
0.040230 0.073520 0.103665 0.036552 0.012478 0.082656 0.037220 0.023362 0.210831 0.009348 0.036056 0.048241 0.010029 0.045909 0.009850 0.053338 0.031021 0.014008 0.106438 0.015248 

Rate = 90.594062
Real rate = 0.905941
0.032345 0.023628 0.252045 0.243150 0.003598 0.033083 0.071027 0.101607 0.036623 0.003141 0.005198 0.047013 0.002403 0.002443 0.009484 0.084836 0.035908 0.000873 0.006725 0.004870 

Rate = 84.702459
Real rate = 0.847025
0.147626 0.033451 0.021197 0.040305 0.003233 0.037155 0.057689 0.033085 0.014639 0.010827 0.025620 0.045135 0.005865 0.004718 0.347371 0.089207 0.048590 0.001636 0.004418 0.028234 

Rate = 83.431372
Real rate = 0.834314
0.103145 0.071775 0.043517 0.038640 0.006176 0.078660 0.092337 0.020234 0.024676 0.037690 0.037628 0.092170 0.016188 0.006767 0.012830 0.095145 0.137857 0.002214 0.008304 0.074045 

Rate = 91.963487
Real rate = 0.919635
0.083754 0.089938 0.051881 0.080487 0.002074 0.145650 0.194776 0.022903 0.026846 0.007408 0.019025 0.145929 0.006740 0.002306 0.008562 0.045574 0.045108 0.001077 0.004933 0.015030 

Rate = 88.912625
Real rate = 0.889126
0.057874 0.013831 0.049142 0.294674 0.001113 0.059825 0.340210 0.029391 0.013982 0.003053 0.006261 0.036337 0.002730 0.001703 0.015611 0.035804 0.024994 0.000866 0.003831 0.008767 

Rate = 78.320719
Real rate = 0.783207
Weight = 1.000000
Finish initial models
in Init_model: 100

. Computing pairwise distances...
KKK

. Building BIONJ tree...
Finish BIONJ tree
ZIP DATA
npatterns:27506
ns:20
notu:113
in model
ncatg : 100
nK : 5
nM : 20
mean diversity : 6.121646
mean reduction factor in alphabet size : 3.267095
mean reduction factor in quadratic computations: 7.353769
ZIP DATA ok
checking memory amount

. This analysis requires at least -1623Mo of memory space.
. Optimisation of the gamma shape parameter and the proportion of invariable sites...


. Starting a SPR cycle... aa
Spr

. (28830 sec)  [-1599634.649657] [Topology           ]
. (29244 sec)  [-1599608.043588] [Topology           ]
. (30864 sec)  [-1599438.028234] [Topology           ]
. (31562 sec)  [-1599431.220815] [Topology           ]
. (32404 sec)  [-1599154.836708] [Topology           ]
. (34285 sec)  [-1599145.001407] [Topology           ]
. (35602 sec)  [-1599104.657526] [Topology           ]
. (35892 sec)  [-1598733.482090] [Topology           ]
. (36464 sec)  [-1598677.237410] [Topology           ]
. (37305 sec)  [-1598671.285945] [Topology           ]
. (39041 sec)  [-1598414.693630] [Topology           ]
. (39186 sec)  [-1598331.723021] [Topology           ]
. (39611 sec)  [-1598294.512211] [Topology           ]
. (41825 sec)  [-1598281.606639] [Topology           ]
. (42668 sec)  [-1598172.213300] [Topology           ]
. (43841 sec)  [-1597907.324753] [Topology           ]
. (44268 sec)  [-1597895.939209] [Topology           ]
. (44989 sec)  [-1597893.725792] [Topology           ]
. (45828 sec)  [-1597682.374777] [Topology           ]
. (46654 sec)  [-1597645.552408] [Topology           ]
. (46929 sec)  [-1597616.029760] [Topology           ]
. (48591 sec)  [-1597576.629466] [Topology           ]
. (51364 sec)  [-1597560.214790] [Topology           ]
. (56792 sec)  [-1597329.167738] [Topology           ]
. (56938 sec)  [-1597281.758828] [Topology           ]
. (57758 sec)  [-1597248.101410] [Topology           ]
. (59845 sec)  [-1597218.463378] [Topology           ]
. (61933 sec)  [-1597136.425463] [Topology           ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (138307 sec)  [-1594378.373106] [Alpha              ][  0.684039]
. (138307 sec)  [-1594378.373106] [P-inv              ][  0.092402]
. (139116 sec)  [-1594146.447575] [Branch lengths     ]

. Starting a SPR cycle... aa
Spr

. (152481 sec)  [-1594114.077757] [Topology           ]
. (152918 sec)  [-1594088.326267] [Topology           ]
. (160888 sec)  [-1594086.539446] [Topology           ]
. (173872 sec)  [-1594062.649897] [Topology           ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (236327 sec)  [-1593677.761646] [Alpha              ][  0.684039]
. (236327 sec)  [-1593677.761646] [P-inv              ][  0.108939]
. (237447 sec)  [-1593632.701096] [Branch lengths     ]

. Starting a SPR cycle... aa
Spr

. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (351698 sec)  [-1593581.307146] [Alpha              ][  0.684039]
. (351698 sec)  [-1593581.307146] [P-inv              ][  0.119833]
. (353491 sec)  [-1593569.067584] [Branch lengths     ]

. Starting simultaneous NNI moves...

. (353609 sec)  [-1593569.067584] [Topology           ]
. (367622 sec)  [-1593517.947899] [Topology           ]
. (383537 sec)  [-1593491.504635] [Topology           ]
. (401257 sec)  [-1593485.412454] [Topology           ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (502144 sec)  [-1593479.215429] [Alpha              ][  0.684039]
. (502144 sec)  [-1593479.215429] [P-inv              ][  0.119833]
. (519899 sec)  [-1593478.355265] [Topology           ]
. (539240 sec)  [-1593477.721966] [Topology           ]
. (559232 sec)  [-1593477.236467] [Topology           ]
. (578937 sec)  [-1593476.905781] [Topology           ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (688918 sec)  [-1593476.495530] [Alpha              ][  0.684039]
. (688918 sec)  [-1593476.495530] [P-inv              ][  0.119833]
. (708832 sec)  [-1593476.405026] [Topology           ]
. (726849 sec)  [-1593476.319297] [Branch lengths     ]
. (745154 sec)  [-1593476.188882] [Branch lengths     ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (852532 sec)  [-1593475.945669] [Alpha              ][  0.684039]
. (852532 sec)  [-1593475.945669] [P-inv              ][  0.119833]
. (870263 sec)  [-1593475.403308] [Branch lengths     ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (974754 sec)  [-1593474.305062] [Alpha              ][  0.684039]
. (974754 sec)  [-1593474.305062] [P-inv              ][  0.119833]
. (991988 sec)  [-1593474.296916] [Branch lengths     ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (1094609 sec)  [-1593474.296916] [Alpha              ][  0.684039]
. (1094609 sec)  [-1593474.296916] [P-inv              ][  0.119833]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (1197190 sec)  [-1593474.296916] [Alpha              ][  0.684039]
. (1197190 sec)  [-1593474.296916] [P-inv              ][  0.119833]

. Checking for NNIs, optimizing five branches...

. Optimisation of the gamma shape parameter and the proportion of invariable sites...


. Starting a SPR cycle... aa
Spr

. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (1682278 sec)  [-1593474.296916] [Alpha              ][  0.684039]
. (1682278 sec)  [-1593474.296916] [P-inv              ][  0.119833]
. (1699175 sec)  [-1593474.296916] [Branch lengths     ]

. Starting simultaneous NNI moves...

. (1699289 sec)  [-1593474.296916] [Topology           ]
. (1717268 sec)  [-1593474.296916] [Topology           ]
. (1734271 sec)  [-1593474.296916] [Branch lengths     ]
. (1751159 sec)  [-1593474.296916] [Branch lengths     ]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (1853750 sec)  [-1593474.296916] [Alpha              ][  0.684039]
. (1853750 sec)  [-1593474.296916] [P-inv              ][  0.119833]
. Optimisation of the gamma shape parameter and the proportion of invariable sites...

. (1956062 sec)  [-1593474.296916] [Alpha              ][  0.684039]
. (1956062 sec)  [-1593474.296916] [P-inv              ][  0.119833]

. Checking for NNIs, optimizing five branches...


. Final log likelihood : -1593474.296916

. Time used 676h48m0s

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