-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathPhyNEST_hc.log
190 lines (178 loc) · 11.8 KB
/
PhyNEST_hc.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
PhyNEST: Phylogenetic Network Estimation using SiTe patterns
Analysis start: 2024-06-02 at 20:03:17
Input file: example/sample_n5h1.txt
Number of sequences: 5
Sequence length: 1000000
Starting Topology: (5,(2,(3,(4,1))));
Outgroup specified for rooting: 5
Number of maximum reticulation(s): 1
The maximum number of iterations for each optimization: 1000
Search algorithm selected: Hill climbing
The maximum number of steps during search: 250000
The maximum number of consecutive failures: 150 (using maximum_number_of_failures provided)
Output file store directory: /Users/khaosan/Dropbox/PhyNESTp.jl
The number of processors for this analysis: 1
(1/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:17
Starting topology changed to (5,(2,((4,3),1))); using nearest-neighbor interchange (NNI)
The search terminated at step 80 and at 75th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 25 proposed, 0 accepted.
Head move of reticulation edge: 25 proposed, 0 accepted.
Change the direction of reticulation edge: 5 proposed, 1 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 23 proposed, 1 accepted.
On the current topology, 96 moves were made, including 21 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(1/10) Estimated topology in this run: (5:3.771,(2:1.117,((1:0.933,(3:0.554,#H6:0.0::1.0):0.38):0.184,(4:0.554)#H6:0.563::0.0):0.0):2.654);
(1/10) Composite likelihood of the estimated topology in this run: 4.830966179213048e6
(2/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
Starting topology changed to (5,((4,3),(2,1))); using nearest-neighbor interchange (NNI)
The search terminated at step 102 and at 101th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 79 proposed, 0 accepted.
Tail move of reticulation edge: 0 proposed, 0 accepted.
Head move of reticulation edge: 0 proposed, 0 accepted.
Change the direction of reticulation edge: 0 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 22 proposed, 0 accepted.
On the current topology, 110 moves were made, including 9 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(2/10) Estimated topology in this run: (5:4.071,((4:1.336,3:1.336):0.0,(2:0.638,1:0.638):0.698):2.736);
(2/10) Composite likelihood of the estimated topology in this run: 4.808939250517486e6
(3/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
Starting topology changed to (5,(1,((4,3),2))); using nearest-neighbor interchange (NNI)
The search terminated at step 105 and at 104th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 81 proposed, 0 accepted.
Tail move of reticulation edge: 0 proposed, 0 accepted.
Head move of reticulation edge: 0 proposed, 0 accepted.
Change the direction of reticulation edge: 0 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 23 proposed, 0 accepted.
On the current topology, 110 moves were made, including 6 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(3/10) Estimated topology in this run: (5:3.865,(1:1.125,((4:1.125,3:1.125):0.0,2:1.125):0.0):2.739);
(3/10) Composite likelihood of the estimated topology in this run: 4.832807714960081e6
(4/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
Starting topology changed to (5,(1,((4,2),3))); using nearest-neighbor interchange (NNI)
The search terminated at step 92 and at 85th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 27 proposed, 1 accepted.
Head move of reticulation edge: 25 proposed, 0 accepted.
Change the direction of reticulation edge: 5 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 33 proposed, 0 accepted.
On the current topology, 96 moves were made, including 11 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(4/10) Estimated topology in this run: (5:4.274,(#H6:0.807::0.0,(((2:0.709,(4:0.709)#H6:0.0::1.0):0.01,3:0.719):0.273,1:0.992):0.523):2.758);
(4/10) Composite likelihood of the estimated topology in this run: 4.817041590497299e6
(5/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
Starting topology changed to (5,(1,(2,(3,4)))); using nearest-neighbor interchange (NNI)
The search terminated at step 106 and at 75th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 29 proposed, 1 accepted.
Head move of reticulation edge: 32 proposed, 0 accepted.
Change the direction of reticulation edge: 10 proposed, 2 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 33 proposed, 1 accepted.
On the current topology, 96 moves were made, including 21 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(5/10) Estimated topology in this run: (5:10.27,(4:5.197,((3:2.358,(2:0.38,#H6:0.0::0.62):1.978):1.273,(1:0.38)#H6:3.25::0.38):1.566):5.073);
(5/10) Composite likelihood of the estimated topology in this run: 4.741352247347821e6
(6/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:20
Starting topology changed to (5,(1,(4,(2,3)))); using nearest-neighbor interchange (NNI)
The search terminated at step 81 and at 75th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 27 proposed, 1 accepted.
Head move of reticulation edge: 25 proposed, 0 accepted.
Change the direction of reticulation edge: 6 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 21 proposed, 0 accepted.
On the current topology, 96 moves were made, including 21 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(6/10) Estimated topology in this run: (5:4.099,(#H6:0.57::0.0,(((2:0.632,3:0.632):0.314,(4:0.946)#H6:0.0::1.0):0.002,1:0.948):0.567):2.584);
(6/10) Composite likelihood of the estimated topology in this run: 4.79908686476507e6
(7/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:20
Starting topology remains unchanged
The search terminated at step 131 and at 75th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 38 proposed, 1 accepted.
Head move of reticulation edge: 42 proposed, 2 accepted.
Change the direction of reticulation edge: 13 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 36 proposed, 1 accepted.
On the current topology, 96 moves were made, including 21 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(7/10) Estimated topology in this run: (5:10.28,(((1:2.363,(2:0.376,(3:0.376)#H6:0.0::0.379):1.988):1.268,#H6:3.255::0.621):1.572,4:5.202):5.077);
(7/10) Composite likelihood of the estimated topology in this run: 4.741362031645942e6
(8/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:32
Starting topology changed to (5,((2,3),(1,4))); using nearest-neighbor interchange (NNI)
The search terminated at step 108 and at 107th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 83 proposed, 0 accepted.
Tail move of reticulation edge: 0 proposed, 0 accepted.
Head move of reticulation edge: 0 proposed, 0 accepted.
Change the direction of reticulation edge: 0 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 24 proposed, 0 accepted.
On the current topology, 111 moves were made, including 4 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(8/10) Estimated topology in this run: (5:4.076,((2:0.638,3:0.638):0.7,(1:1.338,4:1.338):0.0):2.738);
(8/10) Composite likelihood of the estimated topology in this run: 4.808848819713962e6
(9/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:32
Starting topology changed to (5,((3,(1,4)),2)); using nearest-neighbor interchange (NNI)
The search terminated at step 140 and at 86th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 2 proposed, 1 accepted.
Tail move of reticulation edge: 45 proposed, 4 accepted.
Head move of reticulation edge: 34 proposed, 0 accepted.
Change the direction of reticulation edge: 11 proposed, 2 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 47 proposed, 0 accepted.
On the current topology, 96 moves were made, including 10 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(9/10) Estimated topology in this run: (5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);
(9/10) Composite likelihood of the estimated topology in this run: 4.741344634057323e6
(10/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:39
Starting topology changed to (5,(3,(2,(1,4)))); using nearest-neighbor interchange (NNI)
The search terminated at step 79 and at 75th consecutive failures.
Summary of each move:
Insertion of reticulation edge: 1 proposed, 1 accepted.
Tail move of reticulation edge: 26 proposed, 1 accepted.
Head move of reticulation edge: 25 proposed, 0 accepted.
Change the direction of reticulation edge: 5 proposed, 0 accepted.
Deletion of reticulation edge: 0 proposed, 0 accepted.
NNI: 21 proposed, 0 accepted.
On the current topology, 96 moves were made, including 21 unsuccessful moves.
Terminated although it neither reached the maximum number of steps or failures,
possibly because there was no more move to make.
(10/10) Estimated topology in this run: (5:3.743,(#H6:0.425::0.847,((2:0.96,((1:1.385,4:1.385):0.0)#H6:0.0::0.153):0.0,3:0.96):0.425):2.358);
(10/10) Composite likelihood of the estimated topology in this run: 4.822329367341726e6
Summary:
Run Composite likelihood Network estimated
1 4.8309662e6 (5:3.771,(2:1.117,((1:0.933,(3:0.554,#H6:0.0::1.0):0.38):0.184,(4:0.554)#H6:0.563::0.0):0.0):2.654);
2 4.8089393e6 (5:4.071,((4:1.336,3:1.336):0.0,(2:0.638,1:0.638):0.698):2.736);
3 4.8328077e6 (5:3.865,(1:1.125,((4:1.125,3:1.125):0.0,2:1.125):0.0):2.739);
4 4.8170416e6 (5:4.274,(#H6:0.807::0.0,(((2:0.709,(4:0.709)#H6:0.0::1.0):0.01,3:0.719):0.273,1:0.992):0.523):2.758);
5 4.7413522e6 (5:10.27,(4:5.197,((3:2.358,(2:0.38,#H6:0.0::0.62):1.978):1.273,(1:0.38)#H6:3.25::0.38):1.566):5.073);
6 4.7990869e6 (5:4.099,(#H6:0.57::0.0,(((2:0.632,3:0.632):0.314,(4:0.946)#H6:0.0::1.0):0.002,1:0.948):0.567):2.584);
7 4.741362e6 (5:10.28,(((1:2.363,(2:0.376,(3:0.376)#H6:0.0::0.379):1.988):1.268,#H6:3.255::0.621):1.572,4:5.202):5.077);
8 4.8088488e6 (5:4.076,((2:0.638,3:0.638):0.7,(1:1.338,4:1.338):0.0):2.738);
9 4.7413446e6 (5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);
10 4.8223294e6 (5:3.743,(#H6:0.425::0.847,((2:0.96,((1:1.385,4:1.385):0.0)#H6:0.0::0.153):0.0,3:0.96):0.425):2.358);
Best topology: (5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);)
End;