stdout.txt (28322 bytes)
OMP_NUM_THREADS=6
iqtree2 -nt 6 -bb 1000 -bnni -st DNA -s infile.txt --prefix output -p partition_file.txt
IQ-TREE multicore version 2.1.2 COVID-edition for Linux 64-bit built Oct 22 2020
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: exp-1-02 (AVX2, FMA3, 251 GB RAM)
Command: iqtree2 -nt 6 -bb 1000 -bnni -st DNA -s infile.txt --prefix output -p partition_file.txt
Seed: 962455 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Apr 26 11:49:10 2021
Kernel: AVX+FMA - 6 threads (6 CPU cores detected)
Reading partition model file partition_file.txt ...
Reading alignment file infile.txt ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 270 sequences with 700 columns, 403 distinct patterns
227 parsimony-informative, 39 singleton sites, 434 constant sites
Gap/Ambiguity Composition p-value
1 Baabaab3 8.14% passed 88.80%
2 Balter14 6.14% passed 99.60%
3 Balter15 22.86% passed 99.98%
4 Balter16 6.00% passed 99.23%
5 Balter17 15.57% passed 98.64%
6 Balter18 6.00% passed 98.08%
7 Balter19 6.00% passed 100.00%
8 Balter20 6.00% passed 99.95%
9 Balter21 6.00% passed 99.95%
10 Balter22 6.00% passed 99.95%
11 Balter23 10.57% passed 99.98%
12 Balter24 12.86% passed 99.09%
13 Balter25 6.00% passed 99.95%
14 Balter26 6.00% passed 99.95%
15 Balter27 10.29% passed 99.29%
16 Balter28 6.00% passed 99.99%
17 Balter29 6.00% passed 99.43%
18 Balter30 14.29% passed 98.76%
19 Balter31 6.86% passed 99.74%
20 Balter32 12.29% passed 99.31%
21 Balter33 11.29% passed 98.77%
22 Balter34 12.43% passed 98.43%
23 Balter35 6.00% passed 99.36%
24 Balter36 6.00% passed 98.08%
25 Balter37 6.00% passed 98.08%
26 Balter38 6.00% passed 98.08%
27 Balter39 6.00% passed 98.08%
28 Balter40 6.00% passed 98.08%
29 Balter41 6.00% passed 99.95%
30 Balter42 6.00% passed 98.08%
31 Balter43 6.00% passed 98.08%
32 Balter44 6.00% passed 98.08%
33 Balter45 6.00% passed 98.08%
34 Bameri46 6.14% passed 84.57%
35 Bcordi53 12.71% passed 80.00%
36 Bcordi54 6.14% passed 91.69%
37 Bcyano89 9.29% passed 87.24%
38 Bcyano90 6.00% passed 95.79%
39 Bcyano91 6.00% passed 95.79%
40 Bcyano92 6.00% passed 95.79%
41 Bcyano93 6.86% passed 95.80%
42 Bcyano94 9.71% passed 91.41%
43 Bcyano95 6.00% passed 95.79%
44 Bcyano96 6.29% passed 95.38%
45 Bcyano97 6.00% passed 95.79%
46 Bcyano98 6.00% passed 95.79%
47 Bcyano99 6.00% passed 96.87%
48 Bcyan100 14.86% passed 94.88%
49 Bcyan101 28.43% passed 88.59%
50 Bcyan102 9.14% passed 93.71%
51 Bcyan103 9.57% passed 89.54%
52 Bfulm168 6.29% passed 95.32%
53 Bfulm169 6.00% passed 95.51%
54 Bjant217 6.14% passed 96.78%
55 Bjant218 6.14% passed 81.74%
56 Bjant219 20.71% passed 92.01%
57 Bcosti55 6.14% passed 99.06%
58 Bcosti56 6.14% passed 98.69%
59 Bcosti57 6.14% passed 89.99%
60 Bcosti58 6.00% passed 94.60%
61 Bcosti59 6.00% passed 94.60%
62 Bcosti60 6.00% passed 94.60%
63 Bcosti61 6.14% passed 94.93%
64 Bcosti62 6.14% passed 94.93%
65 Bcosti63 41.86% passed 46.83%
66 Bcosti64 41.86% passed 37.99%
67 Bmedi233 6.00% passed 91.54%
68 Bmedi234 6.00% passed 94.37%
69 Bmedi235 6.00% passed 98.20%
70 Bmedi236 6.00% passed 98.93%
71 Bfavi163 6.14% passed 99.31%
72 Bfavi164 6.14% passed 99.76%
73 Bfavi165 6.14% passed 99.72%
74 Bfavi166 6.14% passed 99.80%
75 Bfavi167 6.14% passed 98.35%
76 Bfuma171 6.14% passed 94.97%
77 Bfuma172 24.57% passed 98.72%
78 Bfuma173 6.00% passed 74.34%
79 Bfuma174 6.14% passed 78.66%
80 Bfuma175 6.29% passed 79.78%
81 Bfuma176 11.29% passed 77.96%
82 Bfuma177 11.71% passed 75.23%
83 Bfuma178 6.00% passed 73.18%
84 Bfuma179 6.00% passed 68.66%
85 Bfuma180 16.86% passed 85.83%
86 Bfuma181 6.00% passed 75.42%
87 Bfuma182 8.71% passed 49.31%
88 Bfuma183 11.71% passed 73.21%
89 Bfuma184 6.00% passed 75.42%
90 Bfuma185 6.00% passed 74.83%
91 Bfuma186 6.14% passed 92.59%
92 Bfuma187 6.00% passed 92.12%
93 Bfuma188 6.00% passed 93.89%
94 Bimpe212 11.29% passed 93.64%
95 Bimpe213 7.86% passed 98.71%
96 Bimpe214 19.14% passed 96.68%
97 Bimpe215 12.86% passed 99.28%
98 Bperp258 41.86% passed 83.76%
99 Bperp259 6.00% passed 94.47%
100 Bazure49 6.14% passed 81.90%
101 Bcibol50 20.14% passed 92.84%
102 Bcibol51 6.14% passed 93.86%
103 Bcinct52 13.43% passed 89.15%
104 Bimpo216 6.14% passed 92.60%
105 Bjava220 6.14% passed 80.55%
106 Bjava221 6.00% passed 83.37%
107 Bjava222 6.00% passed 83.37%
108 Bjava223 6.00% passed 83.37%
109 Bjava224 6.00% passed 83.37%
110 Bjava225 45.43% passed 25.94%
111 Bphae261 6.14% passed 96.81%
112 Bphae262 6.14% passed 96.81%
113 Bphae263 6.29% passed 98.02%
114 Bphae264 6.29% passed 96.84%
115 Bphae265 6.00% passed 96.81%
116 Bcyani87 20.43% passed 97.07%
117 Bcyani88 9.14% passed 96.56%
118 Bgala189 8.43% passed 88.45%
119 Bgala190 3.29% passed 80.10%
120 Bgebh191 6.14% passed 96.23%
121 Bgebh192 24.14% passed 94.85%
122 Bgebh193 6.14% passed 96.23%
123 Bgebh194 14.86% passed 97.25%
124 Bgebh195 6.00% passed 98.79%
125 Bgebh196 6.14% passed 97.73%
126 Bgebh197 6.00% passed 98.79%
127 Bgebh198 6.00% passed 98.79%
128 Bgebh199 6.14% passed 96.93%
129 Bkava226 6.00% passed 29.23%
130 Bkava227 6.14% passed 36.05%
131 Bkava228 6.00% passed 30.51%
132 Bkava229 6.00% passed 37.10%
133 Bmexi241 6.14% passed 29.05%
134 Bmexi242 6.14% passed 29.05%
135 Bmexi243 6.14% passed 30.61%
136 Bmexi244 6.14% passed 32.92%
137 Bmexi245 6.14% passed 21.96%
138 Bmexi246 6.14% passed 26.79%
139 Bmexi247 6.71% passed 26.58%
140 Bmexi248 6.14% passed 29.05%
141 Bmexi249 6.14% passed 29.05%
142 Bmexi250 6.14% passed 31.78%
143 Bmexi252 41.86% failed 0.98%
144 Bmexi253 41.86% failed 0.98%
145 Bovip255 6.57% passed 92.69%
146 Bovip256 6.14% passed 99.65%
147 Bnegl254 12.43% passed 81.53%
148 Bquad267 15.86% passed 78.39%
149 Bquad268 6.14% passed 90.28%
150 Bquad269 3.71% passed 97.36%
151 Bquad270 6.00% passed 91.80%
152 Bquad271 6.00% passed 91.80%
153 Bquad272 6.00% passed 91.80%
154 Bquad273 6.00% passed 91.80%
155 Bquad274 7.86% passed 87.30%
156 Bquad275 6.00% passed 91.80%
157 Bquad276 6.00% passed 89.56%
158 Btenu281 6.00% passed 25.79%
159 Bhirs201 6.14% passed 82.49%
160 Bhirs202 6.43% passed 82.73%
161 Bhirs203 6.14% passed 86.56%
162 Bhirs204 6.29% passed 82.08%
163 Bhirs205 6.29% passed 90.73%
164 Bhirs207 41.86% passed 95.89%
165 Bhirs208 6.14% passed 83.05%
166 Bhirs209 42.00% passed 95.37%
167 Bhirs211 6.00% passed 86.44%
168 Bpall257 6.14% passed 89.12%
169 Badusti4 6.14% passed 89.69%
170 Badusti6 6.14% passed 99.77%
171 Badusti7 6.00% passed 99.87%
172 Badusti8 6.00% passed 99.78%
173 Badusti9 10.29% passed 98.34%
174 Badust10 6.00% passed 99.87%
175 Badust11 6.00% passed 99.76%
176 Badust12 6.14% passed 99.99%
177 Baeger13 6.57% passed 99.91%
178 Blate230 6.14% passed 86.79%
179 Blate231 9.71% passed 95.18%
180 Blate232 6.14% passed 90.97%
181 Bcrepi65 6.29% passed 98.85%
182 Bcrepi66 6.00% passed 99.99%
183 Bcrepi67 6.14% passed 99.71%
184 Bcrepi68 6.00% passed 99.43%
185 Bcrepi69 6.00% passed 99.61%
186 Bcrepi70 0.00% passed 96.61%
187 Bcrepi71 6.00% passed 99.95%
188 Bcrepi72 6.00% passed 99.78%
189 Bcrepi73 6.00% passed 99.78%
190 Bcrepi74 6.00% passed 99.78%
191 Bcrepi75 6.00% passed 99.43%
192 Bcrepi76 6.00% passed 99.78%
193 Bcrepi77 6.00% passed 99.90%
194 Bcrepi78 6.00% passed 99.95%
195 Bcrepi79 6.00% passed 99.87%
196 Bcrepi80 6.00% passed 99.78%
197 Bcrepi81 6.00% passed 99.23%
198 Bcrepi82 6.00% passed 99.43%
199 Bcrepi83 6.00% passed 99.23%
200 Bcrepi84 6.00% passed 99.43%
201 Bcrepi85 6.14% passed 99.60%
202 Bcrepi86 6.14% passed 99.60%
203 Bexpl138 6.00% passed 85.04%
204 Bexpl139 6.00% passed 83.32%
205 Bexpl140 6.14% passed 86.17%
206 Bexpl141 6.00% passed 85.04%
207 Bexpl142 6.00% passed 77.47%
208 Bexpl143 6.00% passed 85.04%
209 Bexpl144 6.00% passed 85.04%
210 Bexpl145 10.86% passed 85.50%
211 Bexpl146 6.00% passed 85.04%
212 Bexpl147 6.00% passed 88.62%
213 Bexpl148 6.00% passed 85.04%
214 Bexpl149 6.00% passed 80.71%
215 Bexpl150 6.00% passed 75.68%
216 Bexpl151 6.00% passed 85.04%
217 Bexpl152 6.00% passed 80.71%
218 Bexpl153 6.00% passed 83.32%
219 Bexpl154 6.00% passed 87.61%
220 Bexpl155 6.00% passed 85.04%
221 Bexpl156 6.14% passed 78.73%
222 Bexpl157 6.00% passed 81.82%
223 Bexpl159 6.14% passed 86.05%
224 Bscop279 6.43% passed 99.63%
225 Bsclo278 13.86% passed 98.72%
226 Brachin282 6.57% passed 59.01%
227 Brachin283 6.14% passed 96.28%
228 Brachin284 6.14% passed 92.68%
229 Brachin285 6.14% passed 93.89%
230 Brachin286 6.14% passed 96.11%
231 Brachin287 22.29% passed 77.11%
232 Belon104 6.29% passed 80.40%
233 Belon105 6.14% passed 80.67%
234 Belon106 8.71% passed 91.92%
235 Belon107 6.14% passed 83.93%
236 Belon108 6.14% passed 83.93%
237 Belon109 6.14% passed 80.67%
238 Belon110 6.14% passed 75.12%
239 Belon111 6.14% passed 80.67%
240 Belon112 6.14% passed 80.67%
241 Belon113 6.14% passed 80.67%
242 Belon114 6.14% passed 83.93%
243 Belon115 6.57% passed 80.93%
244 Belon116 12.14% passed 89.25%
245 Belon117 6.00% passed 79.92%
246 Belon118 6.00% passed 84.02%
247 Belon119 6.00% passed 84.02%
248 Belon120 6.00% passed 79.92%
249 Belon121 9.57% passed 85.24%
250 Belon122 6.00% passed 79.92%
251 Belon123 6.00% passed 76.36%
252 Belon124 6.00% passed 79.92%
253 Belon125 41.86% passed 95.65%
254 Belon126 41.86% passed 96.39%
255 Belon127 41.86% passed 92.65%
256 Belon128 6.14% passed 88.16%
257 Belon129 41.86% passed 91.66%
258 Belon130 16.00% passed 75.11%
259 Belon131 15.43% passed 77.73%
260 Belon132 15.43% passed 77.73%
261 Belon133 15.29% passed 75.54%
262 Belon134 6.00% passed 84.02%
263 Belon135 6.00% passed 79.92%
264 Belon136 6.00% passed 84.02%
265 Bgeni200 6.14% passed 83.93%
266 Bhirs210 41.86% passed 93.83%
267 Bmedi237 6.00% passed 94.51%
268 Bmedi238 6.00% passed 95.79%
269 Bmedi239 6.00% passed 95.79%
270 Bmedi240 6.00% passed 95.35%
**** TOTAL 9.20% 2 sequences failed composition chi2 test (p-value<5%; df=3)
Loading 3 partitions...
Subset Type Seqs Sites Infor Invar Model Name
1 DNA 270 234 189 32 TIM2+F+G4 COI_Codon_3
2 DNA 270 233 34 184 TNe+I+G4 COI_Codon_1
3 DNA 270 233 4 218 HKY+F+I COI_Codon_2
Degree of missing data: 0.000
Info: multi-threading strategy over alignment sites
NOTE: Balter36 is identical to Balter18 but kept for subsequent analysis
NOTE: Balter22 is identical to Balter20 but kept for subsequent analysis
NOTE: Bcyano91 is identical to Bcyano90 but kept for subsequent analysis
NOTE: Bcosti59 is identical to Bcosti58 but kept for subsequent analysis
NOTE: Bjava222 is identical to Bjava221 but kept for subsequent analysis
NOTE: Bphae262 is identical to Bphae261 but kept for subsequent analysis
NOTE: Bgebh193 is identical to Bgebh191 but kept for subsequent analysis
NOTE: Bgebh197 is identical to Bgebh195 but kept for subsequent analysis
NOTE: Bmexi242 is identical to Bmexi241 but kept for subsequent analysis
NOTE: Bmexi253 is identical to Bmexi252 but kept for subsequent analysis
NOTE: Bquad271 is identical to Bquad270 but kept for subsequent analysis
NOTE: Bcrepi75 is identical to Bcrepi68 but kept for subsequent analysis
NOTE: Bcrepi73 is identical to Bcrepi72 but kept for subsequent analysis
NOTE: Bcrepi76 is identical to Bcrepi74 but kept for subsequent analysis
NOTE: Bcrepi83 is identical to Bcrepi81 but kept for subsequent analysis
NOTE: Bcrepi86 is identical to Bcrepi85 but kept for subsequent analysis
NOTE: Bexpl144 is identical to Bexpl138 but kept for subsequent analysis
NOTE: Bexpl153 is identical to Bexpl139 but kept for subsequent analysis
NOTE: Belon109 is identical to Belon105 but kept for subsequent analysis
NOTE: Belon108 is identical to Belon107 but kept for subsequent analysis
NOTE: Belon120 is identical to Belon117 but kept for subsequent analysis
NOTE: Belon119 is identical to Belon118 but kept for subsequent analysis
NOTE: Belon132 is identical to Belon131 but kept for subsequent analysis
NOTE: 38 identical sequences (see below) will be ignored for subsequent analysis
NOTE: Balter37 (identical to Balter18) is ignored but added at the end
NOTE: Balter38 (identical to Balter18) is ignored but added at the end
NOTE: Balter39 (identical to Balter18) is ignored but added at the end
NOTE: Balter40 (identical to Balter18) is ignored but added at the end
NOTE: Balter42 (identical to Balter18) is ignored but added at the end
NOTE: Balter43 (identical to Balter18) is ignored but added at the end
NOTE: Balter44 (identical to Balter18) is ignored but added at the end
NOTE: Balter45 (identical to Balter18) is ignored but added at the end
NOTE: Balter26 (identical to Balter20) is ignored but added at the end
NOTE: Bcyano92 (identical to Bcyano90) is ignored but added at the end
NOTE: Bcyano95 (identical to Bcyano90) is ignored but added at the end
NOTE: Bcyano97 (identical to Bcyano90) is ignored but added at the end
NOTE: Bcyano98 (identical to Bcyano90) is ignored but added at the end
NOTE: Bmedi238 (identical to Bcyano90) is ignored but added at the end
NOTE: Bmedi239 (identical to Bcyano90) is ignored but added at the end
NOTE: Bcosti60 (identical to Bcosti58) is ignored but added at the end
NOTE: Bjava223 (identical to Bjava221) is ignored but added at the end
NOTE: Bjava224 (identical to Bjava221) is ignored but added at the end
NOTE: Bgebh198 (identical to Bgebh195) is ignored but added at the end
NOTE: Bmexi248 (identical to Bmexi241) is ignored but added at the end
NOTE: Bmexi249 (identical to Bmexi241) is ignored but added at the end
NOTE: Bquad272 (identical to Bquad270) is ignored but added at the end
NOTE: Bquad273 (identical to Bquad270) is ignored but added at the end
NOTE: Bquad275 (identical to Bquad270) is ignored but added at the end
NOTE: Bcrepi82 (identical to Bcrepi68) is ignored but added at the end
NOTE: Bcrepi84 (identical to Bcrepi68) is ignored but added at the end
NOTE: Bcrepi80 (identical to Bcrepi72) is ignored but added at the end
NOTE: Bexpl146 (identical to Bexpl138) is ignored but added at the end
NOTE: Bexpl148 (identical to Bexpl138) is ignored but added at the end
NOTE: Bexpl151 (identical to Bexpl138) is ignored but added at the end
NOTE: Bexpl155 (identical to Bexpl138) is ignored but added at the end
NOTE: Belon111 (identical to Belon105) is ignored but added at the end
NOTE: Belon112 (identical to Belon105) is ignored but added at the end
NOTE: Belon113 (identical to Belon105) is ignored but added at the end
NOTE: Belon114 (identical to Belon107) is ignored but added at the end
NOTE: Belon122 (identical to Belon117) is ignored but added at the end
NOTE: Belon135 (identical to Belon117) is ignored but added at the end
NOTE: Belon134 (identical to Belon118) is ignored but added at the end
Alignment was printed to output.uniqueseq.phy
For your convenience alignment with unique sequences printed to output.uniqueseq.phy
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 962455)...
NOTE: 13 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -8797.953
Current log-likelihood at step 1: -7574.725
Current log-likelihood at step 2: -7415.142
Current log-likelihood at step 3: -7359.328
Current log-likelihood at step 4: -7342.531
Current log-likelihood at step 5: -7340.426
Current log-likelihood at step 6: -7340.020
Current log-likelihood at step 7: -7339.851
Current log-likelihood at step 8: -7339.750
Current log-likelihood at step 9: -7339.691
Partition-specific rates: 2.551 0.279 0.163
Parameters optimization took 8 rounds (1.164 sec)
Computing ML distances based on estimated model parameters...
Computing ML distances took 0.001165 sec (of wall-clock time) 0.006914 sec(of CPU time)
Computing RapidNJ tree took 0.008509 sec (of wall-clock time) 0.013138 sec (of CPU time)
Log-likelihood of RapidNJ tree: -25897.638
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 2.967 second
Computing log-likelihood of 98 initial trees ... 3.692 seconds
Current best score: -7316.093
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7272.160
Current log-likelihood at step 1: -7271.643
Current log-likelihood at step 2: -7271.543
Parameters optimization took 1 rounds (0.163 sec)
BETTER TREE FOUND at iteration 1: -7271.543
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7271.238
Current log-likelihood at step 1: -7271.124
Current log-likelihood at step 2: -7271.106
Parameters optimization took 1 rounds (0.148 sec)
BETTER TREE FOUND at iteration 9: -7271.106
Iteration 10 / LogL: -7279.842 / Time: 0h:0m:33s
Iteration 20 / LogL: -7275.594 / Time: 0h:0m:58s
Finish initializing candidate tree set (20)
Current best tree score: -7271.106 / CPU time: 56.172
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7270.593
Current log-likelihood at step 1: -7270.562
Parameters optimization took 0 rounds (0.068 sec)
BETTER TREE FOUND at iteration 25: -7270.562
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7267.197
Current log-likelihood at step 1: -7267.187
Parameters optimization took 0 rounds (0.067 sec)
BETTER TREE FOUND at iteration 27: -7267.187
Iteration 30 / LogL: -7271.584 / Time: 0h:1m:17s (0h:4m:18s left)
Iteration 40 / LogL: -7278.991 / Time: 0h:1m:35s (0h:3m:33s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7266.798
Current log-likelihood at step 1: -7266.789
Parameters optimization took 0 rounds (0.067 sec)
BETTER TREE FOUND at iteration 48: -7266.789
Iteration 50 / LogL: -7358.933 / Time: 0h:1m:52s (0h:3m:45s left)
Iteration 60 / LogL: -7296.711 / Time: 0h:2m:9s (0h:3m:13s left)
Iteration 70 / LogL: -7285.055 / Time: 0h:2m:30s (0h:2m:49s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7266.183
Current log-likelihood at step 1: -7266.171
Parameters optimization took 0 rounds (0.064 sec)
BETTER TREE FOUND at iteration 73: -7266.171
Iteration 80 / LogL: -7266.831 / Time: 0h:2m:48s (0h:3m:17s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7265.297
Current log-likelihood at step 1: -7265.287
Parameters optimization took 0 rounds (0.065 sec)
BETTER TREE FOUND at iteration 82: -7265.287
Iteration 90 / LogL: -7265.906 / Time: 0h:3m:4s (0h:3m:10s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7264.656
Current log-likelihood at step 1: -7264.638
Parameters optimization took 0 rounds (0.070 sec)
BETTER TREE FOUND at iteration 91: -7264.638
Iteration 100 / LogL: -7274.659 / Time: 0h:3m:23s (0h:3m:6s left)
Iteration 110 / LogL: -7264.641 / Time: 0h:3m:38s (0h:2m:42s left)
Iteration 120 / LogL: -7269.937 / Time: 0h:3m:55s (0h:2m:20s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7264.461
Current log-likelihood at step 1: -7264.459
Parameters optimization took 0 rounds (0.057 sec)
BETTER TREE FOUND at iteration 128: -7264.459
Iteration 130 / LogL: -7274.138 / Time: 0h:4m:13s (0h:3m:12s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7264.244
Current log-likelihood at step 1: -7264.242
Parameters optimization took 0 rounds (0.057 sec)
BETTER TREE FOUND at iteration 139: -7264.242
Iteration 140 / LogL: -7266.261 / Time: 0h:4m:31s (0h:3m:13s left)
Iteration 150 / LogL: -7281.425 / Time: 0h:4m:48s (0h:2m:52s left)
Iteration 160 / LogL: -7267.456 / Time: 0h:5m:4s (0h:2m:31s left)
BETTER TREE FOUND at iteration 162: -7264.241
Iteration 170 / LogL: -7304.065 / Time: 0h:5m:21s (0h:2m:54s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7264.214
Current log-likelihood at step 1: -7264.207
Parameters optimization took 0 rounds (0.063 sec)
BETTER TREE FOUND at iteration 174: -7264.207
Iteration 180 / LogL: -7265.847 / Time: 0h:5m:38s (0h:2m:57s left)
Iteration 190 / LogL: -7269.005 / Time: 0h:5m:54s (0h:2m:37s left)
Iteration 200 / LogL: -7264.245 / Time: 0h:6m:11s (0h:2m:18s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7263.175
Current log-likelihood at step 1: -7263.149
Parameters optimization took 0 rounds (0.068 sec)
BETTER TREE FOUND at iteration 205: -7263.149
Iteration 210 / LogL: -7266.637 / Time: 0h:6m:30s (0h:2m:57s left)
Iteration 220 / LogL: -7263.913 / Time: 0h:6m:46s (0h:2m:37s left)
Iteration 230 / LogL: -7267.209 / Time: 0h:7m:3s (0h:2m:18s left)
Iteration 240 / LogL: -7264.476 / Time: 0h:7m:20s (0h:1m:59s left)
Iteration 250 / LogL: -7267.268 / Time: 0h:7m:35s (0h:1m:40s left)
Iteration 260 / LogL: -7287.179 / Time: 0h:7m:51s (0h:1m:21s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7263.092
Current log-likelihood at step 1: -7263.088
Parameters optimization took 0 rounds (0.059 sec)
BETTER TREE FOUND at iteration 263: -7263.088
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -7262.995
Current log-likelihood at step 1: -7262.992
Parameters optimization took 0 rounds (0.058 sec)
BETTER TREE FOUND at iteration 270: -7262.992
Iteration 270 / LogL: -7262.992 / Time: 0h:8m:9s (0h:3m:1s left)
Iteration 280 / LogL: -7273.090 / Time: 0h:8m:25s (0h:2m:42s left)
BETTER TREE FOUND at iteration 281: -7262.991
Iteration 290 / LogL: -7271.823 / Time: 0h:8m:41s (0h:2m:44s left)
Iteration 300 / LogL: -7282.627 / Time: 0h:8m:58s (0h:2m:25s left)
BETTER TREE FOUND at iteration 310: -7262.988
Iteration 310 / LogL: -7262.988 / Time: 0h:9m:14s (0h:2m:59s left)
Iteration 320 / LogL: -7268.242 / Time: 0h:9m:28s (0h:2m:40s left)
Iteration 330 / LogL: -7265.095 / Time: 0h:9m:44s (0h:2m:22s left)
Iteration 340 / LogL: -7264.286 / Time: 0h:10m:0s (0h:2m:4s left)
Iteration 350 / LogL: -7263.150 / Time: 0h:10m:16s (0h:1m:46s left)
Iteration 360 / LogL: -7285.948 / Time: 0h:10m:33s (0h:1m:28s left)
Iteration 370 / LogL: -7289.373 / Time: 0h:10m:50s (0h:1m:10s left)
Iteration 380 / LogL: -7280.482 / Time: 0h:11m:8s (0h:0m:52s left)
Iteration 390 / LogL: -7262.994 / Time: 0h:11m:23s (0h:0m:35s left)
Iteration 400 / LogL: -7264.266 / Time: 0h:11m:40s (0h:0m:17s left)
Iteration 410 / LogL: -7267.579 / Time: 0h:11m:59s (0h:0m:0s left)
Refining ufboot trees with NNI 5 branches...
100 samples done
200 samples done
300 samples done
400 samples done
500 samples done
600 samples done
700 samples done
800 samples done
900 samples done
1000 samples done
Total 1000 ufboot trees refined
TREE SEARCH COMPLETED AFTER 411 ITERATIONS / Time: 0h:19m:30s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Initial log-likelihood: -7262.988
Current log-likelihood at step 1: -7262.987
Partition-specific rates: 2.577 0.252 0.165
Parameters optimization took 0 rounds (0.056 sec)
Partition information was printed to output.best_model.nex
BEST SCORE FOUND : -7262.987
Creating bootstrap support values...
Split supports printed to NEXUS file output.splits.nex
Total tree length: 3.613
Total number of iterations: 411
CPU time used for tree search: 4660.646 sec (1h:17m:40s)
Wall-clock time used for tree search: 1168.518 sec (0h:19m:28s)
Total CPU time used: 4673.964 sec (1h:17m:53s)
Total wall-clock time used: 1171.159 sec (0h:19m:31s)
UFBoot trees printed to output.ufboot
Computing bootstrap consensus tree...
Reading input file output.splits.nex...
232 taxa and 6931 splits.
Consensus tree written to output.contree
Reading input trees file output.contree
Log-likelihood of consensus tree: -7263.224
Analysis results written to:
IQ-TREE report: output.iqtree
Maximum-likelihood tree: output.treefile
Likelihood distances: output.mldist
Ultrafast bootstrap approximation results written to:
Split support values: output.splits.nex
Consensus tree: output.contree
UFBoot trees: output.ufboot
Screen log file: output.log
Date and Time: Mon Apr 26 12:08:43 2021