stdout.txt (34504 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-1-03 (AVX2, FMA3, 251 GB RAM)
Command: iqtree2 -nt 6 -bb 1000 -bnni -st DNA -s infile.txt --prefix output -p partition_file.txt
Seed: 61294 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Apr 26 13:36:55 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 282 sequences with 2450 columns, 955 distinct patterns
544 parsimony-informative, 143 singleton sites, 1763 constant sites
Gap/Ambiguity Composition p-value
1 Balter14 2.61% failed 3.92%
2 Bameri46 16.61% passed 8.11%
3 Bfulm168 4.16% passed 6.80%
4 Bjant217 4.94% failed 1.72%
5 Bfavi163 3.59% failed 3.18%
6 Bfuma171 3.59% failed 2.59%
7 Bfuma186 4.24% failed 2.55%
8 Bazure49 4.16% passed 6.65%
9 Bimpo216 3.55% passed 7.42%
10 Bphae261 4.61% passed 7.10%
11 Bphae262 4.12% passed 6.61%
12 Bphae263 4.12% passed 6.61%
13 Bphae264 5.31% failed 4.09%
14 Bgebh193 2.29% passed 9.42%
15 Bmexi245 3.51% passed 13.40%
16 Bmexi246 3.18% passed 14.72%
17 Bmexi247 5.39% passed 10.62%
18 Bmexi249 3.51% passed 12.79%
19 Bnegl254 6.00% passed 16.10%
20 Bquad267 6.94% passed 11.97%
21 Bquad268 4.12% passed 8.47%
22 Bhirs201 4.29% passed 7.69%
23 Bhirs204 4.04% passed 8.52%
24 Bhirs205 4.65% passed 8.30%
25 Bpall257 5.63% passed 5.58%
26 Baeger13 4.33% passed 12.04%
27 Blate230 3.14% failed 3.19%
28 Blate232 4.24% failed 2.43%
29 Bcrepi65 28.29% passed 10.17%
30 Brachin283 6.12% passed 12.13%
31 Brachin284 18.98% passed 5.14%
32 Brachin285 6.33% passed 20.43%
33 Belon105 4.69% failed 4.03%
34 Belon112 2.90% passed 5.84%
35 Bgeni200 5.67% failed 4.95%
36 Bameri47 30.61% failed 0.06%
37 Bsubl280 31.84% failed 0.04%
38 Bfavi161 30.94% failed 0.04%
39 Bfavi162 30.69% failed 0.05%
40 Bmexi251 30.04% failed 0.07%
41 Belon137 46.90% failed 0.86%
42 Bcordi53 32.82% passed 43.12%
43 Bjant218 32.33% passed 43.37%
44 Bfuma172 36.94% passed 61.07%
45 Bgebh191 29.96% passed 30.61%
46 Bgebh194 36.00% passed 21.88%
47 Bmexi248 30.94% passed 94.35%
48 Bovip255 32.98% passed 35.31%
49 Bhirs203 31.63% passed 62.72%
50 Blate231 32.16% passed 32.04%
51 Bhirs206 58.45% passed 22.00%
52 Badusti5 62.49% passed 7.80%
53 Barmig48 58.69% passed 13.51%
54 Brachin288 56.98% passed 11.74%
55 Bcordi54 45.51% passed 27.54%
56 Bcosti55 45.51% passed 40.95%
57 Bcosti56 45.51% passed 45.07%
58 Bcosti57 45.51% passed 53.12%
59 Bfavi164 45.51% passed 41.31%
60 Bjava220 45.51% passed 61.32%
61 Bmexi241 45.84% passed 32.67%
62 Bmexi242 45.80% passed 29.63%
63 Bmexi243 45.63% passed 42.08%
64 Bmexi244 45.55% passed 23.74%
65 Bmexi250 45.51% passed 37.04%
66 Bovip256 45.55% passed 34.02%
67 Bhirs202 45.63% passed 38.75%
68 Badusti4 45.51% passed 44.82%
69 Bscop279 45.59% passed 51.22%
70 Brachin282 45.71% passed 55.49%
71 Brachin286 45.51% passed 40.15%
72 Belon104 45.55% passed 39.39%
73 Belon106 46.24% passed 35.72%
74 Belon107 45.63% passed 43.76%
75 Belon108 45.63% passed 43.76%
76 Belon109 45.63% passed 44.29%
77 Belon110 45.63% passed 43.46%
78 Belon111 45.63% passed 44.29%
79 Belon113 45.63% passed 44.29%
80 Belon114 45.51% passed 41.19%
81 Belon115 45.76% passed 48.94%
82 BBrach1 72.53% failed 0.37%
83 BBrach2 72.33% failed 0.88%
84 Baabaab3 74.04% passed 37.32%
85 Balter15 77.96% passed 57.79%
86 Balter16 73.18% passed 49.18%
87 Balter17 75.88% passed 54.98%
88 Balter18 73.18% passed 48.77%
89 Balter19 73.18% passed 49.05%
90 Balter20 73.18% passed 48.51%
91 Balter21 73.18% passed 48.51%
92 Balter22 73.18% passed 48.51%
93 Balter23 74.49% passed 54.35%
94 Balter24 75.14% passed 49.94%
95 Balter25 73.18% passed 47.46%
96 Balter26 73.18% passed 48.51%
97 Balter27 74.41% passed 59.69%
98 Balter28 73.18% passed 47.99%
99 Balter29 73.18% passed 48.05%
100 Balter30 75.55% passed 64.74%
101 Balter31 73.43% passed 55.42%
102 Balter32 74.98% passed 43.10%
103 Balter33 74.69% passed 42.28%
104 Balter34 75.02% passed 45.00%
105 Balter35 73.18% passed 49.72%
106 Balter36 73.18% passed 48.77%
107 Balter37 73.18% passed 48.77%
108 Balter38 73.18% passed 48.77%
109 Balter39 73.18% passed 48.77%
110 Balter40 73.18% passed 48.77%
111 Balter41 73.18% passed 47.46%
112 Balter42 73.18% passed 48.77%
113 Balter43 73.18% passed 48.77%
114 Balter44 73.18% passed 48.77%
115 Balter45 73.18% passed 48.77%
116 Bcyano89 74.08% passed 91.55%
117 Bcyano90 73.18% passed 70.79%
118 Bcyano91 73.18% passed 70.79%
119 Bcyano92 73.18% passed 70.79%
120 Bcyano93 73.39% passed 79.15%
121 Bcyano94 74.20% passed 85.11%
122 Bcyano95 73.18% passed 70.79%
123 Bcyano96 73.27% passed 70.66%
124 Bcyano97 73.18% passed 70.79%
125 Bcyano98 73.18% passed 70.79%
126 Bcyano99 73.18% passed 71.46%
127 Bcyan100 75.67% passed 75.97%
128 Bcyan101 79.55% passed 23.13%
129 Bcyan102 74.08% passed 85.15%
130 Bcyan103 74.20% passed 89.41%
131 Bfulm169 73.18% passed 49.04%
132 Bjant219 77.35% passed 88.95%
133 Bcosti58 73.18% passed 31.52%
134 Bcosti59 73.18% passed 31.52%
135 Bcosti60 73.18% passed 31.52%
136 Bcosti61 73.18% passed 31.63%
137 Bcosti62 73.18% passed 31.63%
138 Bcosti63 83.39% passed 7.86%
139 Bcosti64 83.39% passed 5.81%
140 Bmedi233 73.18% passed 54.30%
141 Bmedi234 73.18% passed 54.50%
142 Bmedi235 73.18% passed 61.59%
143 Bmedi236 73.18% passed 61.41%
144 Bfavi165 73.18% passed 61.14%
145 Bfavi166 73.18% passed 62.47%
146 Bfavi167 73.18% passed 60.73%
147 Bfuma173 73.18% passed 49.51%
148 Bfuma174 73.22% passed 60.58%
149 Bfuma175 73.27% passed 56.91%
150 Bfuma176 74.65% passed 58.84%
151 Bfuma177 74.78% passed 51.42%
152 Bfuma178 73.18% passed 49.74%
153 Bfuma179 73.18% passed 44.62%
154 Bfuma180 76.24% passed 50.64%
155 Bfuma181 73.18% passed 56.22%
156 Bfuma182 73.92% passed 53.26%
157 Bfuma183 74.78% passed 43.34%
158 Bfuma184 73.18% passed 56.22%
159 Bfuma185 73.18% passed 48.80%
160 Bfuma187 73.18% passed 83.70%
161 Bfuma188 73.18% passed 81.37%
162 Bimpe212 74.69% passed 47.86%
163 Bimpe213 73.71% passed 67.11%
164 Bimpe214 76.90% passed 33.86%
165 Bimpe215 75.14% passed 57.07%
166 Bperp258 83.39% passed 23.66%
167 Bperp259 73.18% passed 55.91%
168 Bcibol50 77.18% passed 37.37%
169 Bcibol51 73.18% passed 57.44%
170 Bcinct52 75.27% passed 78.26%
171 Bjava221 73.18% passed 22.85%
172 Bjava222 73.18% passed 22.85%
173 Bjava223 73.18% passed 22.85%
174 Bjava224 73.18% passed 22.85%
175 Bjava225 84.41% failed 4.89%
176 Bphae265 73.18% passed 40.99%
177 Bcyani87 77.27% passed 49.96%
178 Bcyani88 74.08% passed 76.16%
179 Bgala189 74.16% passed 44.93%
180 Bgala190 73.39% passed 24.08%
181 Bgebh192 78.33% passed 45.17%
182 Bgebh195 73.18% passed 32.03%
183 Bgebh196 73.18% passed 29.92%
184 Bgebh197 73.18% passed 32.03%
185 Bgebh198 73.18% passed 32.03%
186 Bgebh199 73.18% passed 29.52%
187 Bkava226 73.18% failed 4.47%
188 Bkava227 73.18% passed 6.32%
189 Bkava228 73.18% passed 5.06%
190 Bkava229 73.18% passed 5.67%
191 Bmexi252 83.39% failed 0.08%
192 Bmexi253 83.39% failed 0.08%
193 Bquad269 73.27% passed 56.31%
194 Bquad270 73.18% passed 49.44%
195 Bquad271 73.18% passed 49.44%
196 Bquad272 73.18% passed 49.44%
197 Bquad273 73.18% passed 49.44%
198 Bquad274 73.67% passed 61.80%
199 Bquad275 73.18% passed 49.44%
200 Bquad276 73.18% passed 51.52%
201 Btenu281 73.18% passed 5.42%
202 Bhirs207 83.39% passed 38.98%
203 Bhirs208 73.18% passed 46.15%
204 Bhirs209 83.43% passed 39.23%
205 Bhirs211 73.18% passed 47.99%
206 Badusti6 73.22% passed 50.93%
207 Badusti7 73.18% passed 49.64%
208 Badusti8 73.18% passed 49.09%
209 Badusti9 74.41% passed 59.47%
210 Badust10 73.18% passed 49.64%
211 Badust11 73.18% passed 49.67%
212 Badust12 73.18% passed 47.99%
213 Bcrepi66 73.18% passed 47.99%
214 Bcrepi67 73.22% passed 47.36%
215 Bcrepi68 73.18% passed 48.05%
216 Bcrepi69 73.18% passed 44.98%
217 Bcrepi70 73.18% passed 49.09%
218 Bcrepi71 73.18% passed 48.51%
219 Bcrepi72 73.18% passed 49.09%
220 Bcrepi73 73.18% passed 49.09%
221 Bcrepi74 73.18% passed 49.09%
222 Bcrepi75 73.18% passed 48.05%
223 Bcrepi76 73.18% passed 49.09%
224 Bcrepi77 73.18% passed 57.29%
225 Bcrepi78 73.18% passed 48.51%
226 Bcrepi79 73.18% passed 49.64%
227 Bcrepi80 73.18% passed 49.09%
228 Bcrepi81 73.18% passed 49.18%
229 Bcrepi82 73.18% passed 48.05%
230 Bcrepi83 73.18% passed 49.18%
231 Bcrepi84 73.18% passed 48.05%
232 Bcrepi85 73.18% passed 49.09%
233 Bcrepi86 73.18% passed 49.09%
234 Bexpl138 73.18% passed 26.81%
235 Bexpl139 73.18% passed 25.44%
236 Bexpl140 73.22% passed 28.58%
237 Bexpl141 73.18% passed 26.81%
238 Bexpl142 73.18% passed 23.20%
239 Bexpl143 73.18% passed 26.81%
240 Bexpl144 73.18% passed 26.81%
241 Bexpl145 74.57% passed 27.10%
242 Bexpl146 73.18% passed 26.81%
243 Bexpl147 73.18% passed 29.07%
244 Bexpl148 73.18% passed 26.81%
245 Bexpl149 73.18% passed 24.44%
246 Bexpl150 73.18% passed 22.01%
247 Bexpl151 73.18% passed 26.81%
248 Bexpl152 73.18% passed 24.44%
249 Bexpl153 73.18% passed 25.44%
250 Bexpl154 73.18% passed 27.90%
251 Bexpl155 73.18% passed 26.81%
252 Bexpl156 73.18% passed 23.20%
253 Bexpl157 73.18% passed 25.46%
254 Bexpl159 73.18% passed 26.81%
255 Bsclo278 75.39% passed 53.97%
256 Brachin287 77.80% passed 58.05%
257 Belon116 74.90% passed 82.30%
258 Belon117 73.18% passed 40.76%
259 Belon118 73.18% passed 43.43%
260 Belon119 73.18% passed 43.43%
261 Belon120 73.18% passed 40.76%
262 Belon121 74.20% passed 64.06%
263 Belon122 73.18% passed 40.76%
264 Belon123 73.18% passed 37.76%
265 Belon124 73.18% passed 40.76%
266 Belon125 83.39% passed 38.51%
267 Belon126 83.39% passed 40.38%
268 Belon127 83.39% passed 32.72%
269 Belon128 73.18% passed 42.86%
270 Belon129 83.39% passed 34.07%
271 Belon130 76.00% passed 31.36%
272 Belon131 75.84% passed 36.14%
273 Belon132 75.84% passed 36.14%
274 Belon133 75.80% passed 37.16%
275 Belon134 73.18% passed 43.43%
276 Belon135 73.18% passed 40.76%
277 Belon136 73.18% passed 43.43%
278 Bhirs210 83.39% passed 34.28%
279 Bmedi237 73.18% passed 68.04%
280 Bmedi238 73.18% passed 70.79%
281 Bmedi239 73.18% passed 70.79%
282 Bmedi240 73.18% passed 68.68%
WARNING: 205 sequences contain more than 50% gaps/ambiguity
**** TOTAL 60.66% 22 sequences failed composition chi2 test (p-value<5%; df=3)
Loading 7 partitions...
Subset Type Seqs Sites Infor Invar Model Name
1 DNA 270 219 34 170 TNe+I+G4 COI_Codon_1
2 DNA 270 219 4 204 HKY+F+I COI_Codon_2
3 DNA 270 219 189 20 TIM2+F+G4 COI_Codon_3
4 DNA 70 226 22 198 HKY+F+I CAD_Codon_1
5 DNA 70 226 4 216 TN+F CAD_Codon_2
6 DNA 70 226 102 100 HKY+F+G4 CAD_Codon_3
7 DNA 54 1115 189 855 GTR+F+R2 28S__from_Phred_Phrap_
Degree of missing data: 0.587
Info: multi-threading strategy over partitions
NOTE: Belon108 is identical to Belon107 but kept for subsequent analysis
NOTE: Belon111 is identical to Belon109 but kept for subsequent analysis
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: Bgebh197 is identical to Bgebh195 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: Bcrepi72 is identical to Bcrepi70 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: Bexpl144 is identical to Bexpl138 but kept for subsequent analysis
NOTE: Bexpl153 is identical to Bexpl139 but kept for subsequent analysis
NOTE: Bexpl159 is identical to Bexpl141 but kept for subsequent analysis
NOTE: Bexpl156 is identical to Bexpl142 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: 36 identical sequences (see below) will be ignored for subsequent analysis
NOTE: Belon113 (identical to Belon109) is ignored but added at the end
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: 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: Bcrepi73 (identical to Bcrepi70) is ignored but added at the end
NOTE: Bcrepi80 (identical to Bcrepi70) is ignored but added at the end
NOTE: Bcrepi85 (identical to Bcrepi70) is ignored but added at the end
NOTE: Bcrepi86 (identical to Bcrepi70) 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: 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)... 0.047 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 61294)...
NOTE: 17 MB RAM (0 GB) is required!
WARNING: Number of threads seems too high for short alignments. Use -T AUTO to determine best number of threads.
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -17172.598
Current log-likelihood at step 1: -15092.097
Current log-likelihood at step 2: -14853.240
Current log-likelihood at step 3: -14714.130
Current log-likelihood at step 4: -14631.838
Current log-likelihood at step 5: -14624.779
Current log-likelihood at step 6: -14622.030
Current log-likelihood at step 7: -14619.994
Current log-likelihood at step 8: -14618.233
Current log-likelihood at step 9: -14616.605
Current log-likelihood at step 10: -14615.075
Current log-likelihood at step 11: -14613.642
Current log-likelihood at step 12: -14612.284
Current log-likelihood at step 13: -14611.010
Current log-likelihood at step 14: -14609.806
Current log-likelihood at step 15: -14608.649
Current log-likelihood at step 16: -14605.154
Current log-likelihood at step 17: -14604.382
Current log-likelihood at step 18: -14603.648
Current log-likelihood at step 19: -14602.944
Current log-likelihood at step 20: -14602.270
Current log-likelihood at step 21: -14601.614
Current log-likelihood at step 22: -14600.990
Current log-likelihood at step 23: -14600.384
Current log-likelihood at step 24: -14599.792
Current log-likelihood at step 25: -14599.223
Current log-likelihood at step 26: -14598.677
Current log-likelihood at step 27: -14598.140
Current log-likelihood at step 28: -14597.606
Current log-likelihood at step 29: -14597.087
Current log-likelihood at step 30: -14596.332
Current log-likelihood at step 31: -14595.848
Current log-likelihood at step 32: -14595.395
Current log-likelihood at step 33: -14594.934
Current log-likelihood at step 34: -14594.491
Current log-likelihood at step 35: -14594.051
Current log-likelihood at step 36: -14593.614
Current log-likelihood at step 37: -14593.173
Current log-likelihood at step 38: -14592.739
Current log-likelihood at step 39: -14592.306
Current log-likelihood at step 40: -14591.874
Current log-likelihood at step 41: -14591.441
Current log-likelihood at step 42: -14591.009
Current log-likelihood at step 43: -14590.577
Current log-likelihood at step 44: -14590.144
Current log-likelihood at step 45: -14589.710
Current log-likelihood at step 46: -14589.276
Current log-likelihood at step 47: -14588.841
Current log-likelihood at step 48: -14588.404
Current log-likelihood at step 49: -14587.966
Current log-likelihood at step 50: -14587.526
Current log-likelihood at step 51: -14587.083
Current log-likelihood at step 52: -14586.638
Current log-likelihood at step 53: -14586.189
Current log-likelihood at step 54: -14585.739
Current log-likelihood at step 55: -14585.282
Current log-likelihood at step 56: -14584.824
Current log-likelihood at step 57: -14584.363
Current log-likelihood at step 58: -14583.898
Current log-likelihood at step 59: -14583.429
Current log-likelihood at step 60: -14582.956
Current log-likelihood at step 61: -14582.469
Current log-likelihood at step 62: -14581.986
Current log-likelihood at step 63: -14581.498
Current log-likelihood at step 64: -14581.004
Current log-likelihood at step 65: -14580.505
Current log-likelihood at step 66: -14580.000
Current log-likelihood at step 67: -14579.489
Current log-likelihood at step 68: -14578.971
Current log-likelihood at step 69: -14578.445
Current log-likelihood at step 70: -14577.911
Current log-likelihood at step 71: -14577.373
Current log-likelihood at step 72: -14576.828
Current log-likelihood at step 73: -14576.264
Current log-likelihood at step 74: -14575.703
Current log-likelihood at step 75: -14575.133
Current log-likelihood at step 76: -14574.551
Current log-likelihood at step 77: -14573.963
Current log-likelihood at step 78: -14573.366
Current log-likelihood at step 79: -14572.760
Current log-likelihood at step 80: -14572.143
Current log-likelihood at step 81: -14571.515
Current log-likelihood at step 82: -14570.877
Current log-likelihood at step 83: -14570.229
Current log-likelihood at step 84: -14569.568
Current log-likelihood at step 85: -14568.896
Current log-likelihood at step 86: -14568.211
Current log-likelihood at step 87: -14567.513
Current log-likelihood at step 88: -14566.801
Current log-likelihood at step 89: -14566.076
Current log-likelihood at step 90: -14565.338
Current log-likelihood at step 91: -14564.581
Current log-likelihood at step 92: -14563.813
Current log-likelihood at step 93: -14563.029
Current log-likelihood at step 94: -14562.225
Current log-likelihood at step 95: -14561.409
Current log-likelihood at step 96: -14560.578
Current log-likelihood at step 97: -14559.720
Current log-likelihood at step 98: -14558.855
Current log-likelihood at step 99: -14557.974
Partition-specific rates: 0.496 0.063 6.072 0.169 0.033 0.890 0.674
Parameters optimization took 99 rounds (9.960 sec)
Computing ML distances based on estimated model parameters...
Computing ML distances took 0.003212 sec (of wall-clock time) 0.019127 sec(of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Computing RapidNJ tree took 0.009714 sec (of wall-clock time) 0.020610 sec (of CPU time)
Log-likelihood of RapidNJ tree: -40086.025
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 5.708 second
Computing log-likelihood of 98 initial trees ... 6.016 seconds
Current best score: -14401.271
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14339.412
Current log-likelihood at step 1: -14337.801
Current log-likelihood at step 2: -14336.925
Current log-likelihood at step 3: -14336.049
Current log-likelihood at step 4: -14335.167
Current log-likelihood at step 5: -14334.273
Current log-likelihood at step 6: -14333.367
Current log-likelihood at step 7: -14332.451
Current log-likelihood at step 8: -14331.527
Current log-likelihood at step 9: -14330.596
Current log-likelihood at step 10: -14329.661
Current log-likelihood at step 11: -14319.233
Current log-likelihood at step 12: -14319.222
Parameters optimization took 11 rounds (1.013 sec)
BETTER TREE FOUND at iteration 1: -14319.222
Iteration 10 / LogL: -14327.730 / Time: 0h:1m:1s
Iteration 20 / LogL: -14325.448 / Time: 0h:1m:37s
Finish initializing candidate tree set (20)
Current best tree score: -14319.222 / CPU time: 86.500
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14315.597
Current log-likelihood at step 1: -14315.302
Current log-likelihood at step 2: -14315.279
Parameters optimization took 1 rounds (0.193 sec)
BETTER TREE FOUND at iteration 21: -14315.279
Iteration 30 / LogL: -14316.322 / Time: 0h:2m:2s (0h:6m:24s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14313.855
Current log-likelihood at step 1: -14313.838
Parameters optimization took 0 rounds (0.107 sec)
BETTER TREE FOUND at iteration 35: -14313.838
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14313.601
Current log-likelihood at step 1: -14313.587
Parameters optimization took 0 rounds (0.081 sec)
BETTER TREE FOUND at iteration 37: -14313.587
Iteration 40 / LogL: -14319.181 / Time: 0h:2m:26s (0h:6m:3s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14312.767
Current log-likelihood at step 1: -14312.708
Parameters optimization took 0 rounds (0.078 sec)
BETTER TREE FOUND at iteration 49: -14312.708
Iteration 50 / LogL: -14437.252 / Time: 0h:2m:46s (0h:5m:35s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14311.374
Current log-likelihood at step 1: -14311.224
Current log-likelihood at step 2: -14311.211
Parameters optimization took 1 rounds (0.221 sec)
BETTER TREE FOUND at iteration 58: -14311.211
Iteration 60 / LogL: -14321.794 / Time: 0h:3m:11s (0h:5m:18s left)
Iteration 70 / LogL: -14343.184 / Time: 0h:3m:35s (0h:4m:34s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14309.773
Current log-likelihood at step 1: -14309.725
Parameters optimization took 0 rounds (0.085 sec)
BETTER TREE FOUND at iteration 72: -14309.725
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14308.928
Current log-likelihood at step 1: -14308.872
Parameters optimization took 0 rounds (0.082 sec)
BETTER TREE FOUND at iteration 76: -14308.872
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14308.824
Current log-likelihood at step 1: -14308.801
Parameters optimization took 0 rounds (0.084 sec)
BETTER TREE FOUND at iteration 79: -14308.801
Iteration 80 / LogL: -14366.948 / Time: 0h:3m:58s (0h:4m:58s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14308.644
Current log-likelihood at step 1: -14308.630
Parameters optimization took 0 rounds (0.077 sec)
BETTER TREE FOUND at iteration 87: -14308.630
Iteration 90 / LogL: -14308.844 / Time: 0h:4m:19s (0h:4m:42s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14308.255
Current log-likelihood at step 1: -14308.244
Parameters optimization took 0 rounds (0.080 sec)
BETTER TREE FOUND at iteration 91: -14308.244
Iteration 100 / LogL: -14310.858 / Time: 0h:4m:42s (0h:4m:19s left)
Iteration 110 / LogL: -14308.315 / Time: 0h:5m:6s (0h:3m:47s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14308.087
Current log-likelihood at step 1: -14308.038
Parameters optimization took 0 rounds (0.101 sec)
BETTER TREE FOUND at iteration 117: -14308.038
Iteration 120 / LogL: -14311.205 / Time: 0h:5m:30s (0h:4m:29s left)
Iteration 130 / LogL: -14308.856 / Time: 0h:5m:55s (0h:3m:59s left)
Iteration 140 / LogL: -14309.447 / Time: 0h:6m:19s (0h:3m:30s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14307.897
Current log-likelihood at step 1: -14307.887
Parameters optimization took 0 rounds (0.087 sec)
BETTER TREE FOUND at iteration 142: -14307.887
Iteration 150 / LogL: -14309.939 / Time: 0h:6m:40s (0h:4m:7s left)
Iteration 160 / LogL: -14309.715 / Time: 0h:7m:4s (0h:3m:38s left)
Iteration 170 / LogL: -14321.709 / Time: 0h:7m:29s (0h:3m:11s left)
Iteration 180 / LogL: -14309.510 / Time: 0h:7m:52s (0h:2m:43s left)
Iteration 190 / LogL: -14311.106 / Time: 0h:8m:16s (0h:2m:16s left)
Iteration 200 / LogL: -14332.760 / Time: 0h:8m:39s (0h:1m:49s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14307.865
Current log-likelihood at step 1: -14307.856
Parameters optimization took 0 rounds (0.109 sec)
BETTER TREE FOUND at iteration 202: -14307.856
Iteration 210 / LogL: -14309.412 / Time: 0h:9m:3s (0h:3m:59s left)
Iteration 220 / LogL: -14321.755 / Time: 0h:9m:24s (0h:3m:31s left)
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -14307.842
Current log-likelihood at step 1: -14307.836
Parameters optimization took 0 rounds (0.080 sec)
BETTER TREE FOUND at iteration 223: -14307.836
Iteration 230 / LogL: -14307.861 / Time: 0h:9m:49s (0h:3m:59s left)
Iteration 240 / LogL: -14314.897 / Time: 0h:10m:12s (0h:3m:32s left)
Iteration 250 / LogL: -14309.976 / Time: 0h:10m:35s (0h:3m:6s left)
Iteration 260 / LogL: -14317.444 / Time: 0h:11m:0s (0h:2m:40s left)
Iteration 270 / LogL: -14308.940 / Time: 0h:11m:24s (0h:2m:14s left)
Iteration 280 / LogL: -14388.274 / Time: 0h:11m:46s (0h:1m:48s left)
BETTER TREE FOUND at iteration 282: -14307.827
BETTER TREE FOUND at iteration 289: -14307.824
Iteration 290 / LogL: -14313.456 / Time: 0h:12m:11s (0h:4m:10s left)
Iteration 300 / LogL: -14316.381 / Time: 0h:12m:35s (0h:3m:44s left)
Iteration 310 / LogL: -14314.106 / Time: 0h:12m:59s (0h:3m:19s left)
Iteration 320 / LogL: -14308.343 / Time: 0h:13m:23s (0h:2m:53s left)
Iteration 330 / LogL: -14308.938 / Time: 0h:13m:46s (0h:2m:28s left)
Iteration 340 / LogL: -14309.642 / Time: 0h:14m:11s (0h:2m:3s left)
Iteration 350 / LogL: -14307.982 / Time: 0h:14m:34s (0h:1m:37s left)
Iteration 360 / LogL: -14310.577 / Time: 0h:14m:57s (0h:1m:12s left)
Iteration 370 / LogL: -14307.848 / Time: 0h:15m:20s (0h:0m:47s left)
Iteration 380 / LogL: -14316.514 / Time: 0h:15m:42s (0h:0m:22s left)
BETTER TREE FOUND at iteration 383: -14307.822
Iteration 390 / LogL: -14309.650 / Time: 0h:16m:8s (0h:3m:51s left)
Iteration 400 / LogL: -14309.641 / Time: 0h:16m:31s (0h:3m:26s left)
Iteration 410 / LogL: -14323.908 / Time: 0h:16m:54s (0h:3m:1s left)
Iteration 420 / LogL: -14310.319 / Time: 0h:17m:16s (0h:2m:35s left)
Iteration 430 / LogL: -14312.621 / Time: 0h:17m:39s (0h:2m:10s left)
Iteration 440 / LogL: -14319.755 / Time: 0h:18m:1s (0h:1m:45s left)
Iteration 450 / LogL: -14313.242 / Time: 0h:18m:22s (0h:1m:20s left)
Iteration 460 / LogL: -14357.311 / Time: 0h:18m:42s (0h:0m:56s left)
Iteration 470 / LogL: -14311.040 / Time: 0h:19m:6s (0h:0m:31s left)
Iteration 480 / LogL: -14309.887 / Time: 0h:19m:31s (0h:0m:7s 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 484 ITERATIONS / Time: 0h:37m:27s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Initial log-likelihood: -14307.822
Current log-likelihood at step 1: -14307.817
Partition-specific rates: 0.479 0.057 6.149 0.165 0.031 0.839 0.675
Parameters optimization took 0 rounds (0.085 sec)
Partition information was printed to output.best_model.nex
BEST SCORE FOUND : -14307.817
Creating bootstrap support values...
Split supports printed to NEXUS file output.splits.nex
Total tree length: 1.948
Total number of iterations: 484
CPU time used for tree search: 13110.701 sec (3h:38m:30s)
Wall-clock time used for tree search: 2236.590 sec (0h:37m:16s)
Total CPU time used: 13174.961 sec (3h:39m:34s)
Total wall-clock time used: 2248.202 sec (0h:37m:28s)
UFBoot trees printed to output.ufboot
Computing bootstrap consensus tree...
Reading input file output.splits.nex...
246 taxa and 8471 splits.
Consensus tree written to output.contree
Reading input trees file output.contree
Log-likelihood of consensus tree: -14310.839
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 14:14:25 2021