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During AU test, 1.6.6&1.6.7 crashes with following error, while 1.6.1 is works fine for both my macOS High Sierra and Ubuntu 14.04 #72

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Kinggerm opened this issue Jul 22, 2018 · 2 comments
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During AU test, 1.6.6&1.6.7 crashes with following error, while 1.6.1 is works fine for both my macOS High Sierra and Ubuntu 14.04 #72

Kinggerm opened this issue Jul 22, 2018 · 2 comments

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@Kinggerm
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Kinggerm commented Jul 22, 2018 •
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IQ-TREE multicore version 1.6.6 for Mac OS X 64-bit built Jul 1 2018
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host: KMBP (AVX2, FMA3, 16 GB RAM)
Command: iqtree -s test.fasta -z no_br.trees -zb 1000 -au -nt 2
Seed: 36129 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Sun Jul 22 16:08:34 2018
Kernel: AVX+FMA - 2 threads (8 CPU cores detected)

Reading alignment file test.fasta ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 4 sequences with 10 columns, 8 distinct patterns
2 parsimony-informative, 3 singleton sites, 5 constant sites
Gap/Ambiguity Composition p-value
1 A 0.00% passed 98.80%
2 B 0.00% passed 74.18%
3 C 0.00% passed 76.05%
4 D 0.00% passed 95.78%
**** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=3)

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 seconds
NOTE: ModelFinder requires 0 MB RAM!
ModelFinder will test 286 DNA models (sample size: 10) ...
No. Model -LnL df AIC AICc BIC
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
1 JC 32.615 5 75.230 90.230 76.743
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
2 JC+I 32.615 6 77.230 105.230 79.045
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
3 JC+G4 32.616 6 77.231 105.231 79.047
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
4 JC+I+G4 32.893 7 79.786 135.786 81.904
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
5 JC+R2 32.628 7 79.256 135.256 81.374
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
6 JC+R3 32.618 9 83.236 263.236 85.959
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
14 F81+F 32.170 8 80.339 224.339 82.760
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
15 F81+F+I 32.170 9 82.339 262.339 85.063
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
16 F81+F+G4 32.171 9 82.341 262.341 85.064
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
17 F81+F+I+G4 32.411 10 84.821 304.821 87.847
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
18 F81+F+R2 32.171 10 84.343 304.343 87.368
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
19 F81+F+R3 32.170 12 88.340 400.340 91.971
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
27 K2P 30.837 6 73.674 101.674 75.489
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
28 K2P+I 30.837 7 75.674 131.674 77.792
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
29 K2P+G4 30.838 7 75.675 131.675 77.794
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
30 K2P+I+G4 31.037 8 78.074 222.074 80.495
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
31 K2P+R2 30.837 8 77.674 221.674 80.095
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
32 K2P+R3 30.837 10 81.674 301.674 84.700
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
40 HKY+F 30.217 9 78.433 258.433 81.156
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
41 HKY+F+I 30.217 10 80.433 300.433 83.459
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
42 HKY+F+G4 30.218 10 80.435 300.435 83.461
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
43 HKY+F+I+G4 30.405 11 82.810 346.810 86.138
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
44 HKY+F+R2 30.217 11 82.433 346.433 85.762
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
45 HKY+F+R3 30.217 13 86.433 450.433 90.367
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
53 TNe 30.837 7 75.674 131.674 77.792
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
54 TNe+I 30.837 8 77.674 221.674 80.094
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
55 TNe+G4 30.838 8 77.675 221.675 80.096
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
56 TNe+I+G4 30.960 9 79.920 259.920 82.643
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
57 TNe+R2 30.837 9 79.674 259.674 82.397
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
58 TNe+R3 30.837 11 83.674 347.674 87.002
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
66 TN+F 30.217 10 80.433 300.433 83.459
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
67 TN+F+I 30.217 11 82.433 346.433 85.762
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
68 TN+F+G4 30.218 11 82.435 346.435 85.764
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
69 TN+F+I+G4 30.336 12 84.671 396.671 88.302
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
70 TN+F+R2 30.217 12 84.433 396.433 88.064
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
71 TN+F+R3 30.217 14 88.433 508.433 92.669
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
79 K3P 30.756 7 75.512 131.512 77.630
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
80 K3P+I 30.725 8 77.450 221.450 79.871
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
81 K3P+G4 30.726 8 77.452 221.452 79.873
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
82 K3P+I+G4 30.804 9 79.607 259.607 82.331
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
83 K3P+R2 30.725 9 79.450 259.450 82.174
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
84 K3P+R3 30.725 11 83.450 347.450 86.779
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
92 K3Pu+F 30.100 10 80.201 300.201 83.227
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
93 K3Pu+F+I 30.100 11 82.201 346.201 85.529
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
94 K3Pu+F+G4 30.101 11 82.203 346.203 85.531
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
95 K3Pu+F+I+G4 30.179 12 84.357 396.357 87.989
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
96 K3Pu+F+R2 30.100 12 84.201 396.201 87.832
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
97 K3Pu+F+R3 30.100 14 88.201 508.201 92.437
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
105 TPM2+F 30.127 10 80.254 300.254 83.279
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
106 TPM2+F+I 30.052 11 82.103 346.103 85.432
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
107 TPM2+F+G4 30.053 11 82.105 346.105 85.434
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
108 TPM2+F+I+G4 30.120 12 84.240 396.240 87.871
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
109 TPM2+F+R2 30.052 12 84.103 396.103 87.734
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
110 TPM2+F+R3 30.052 14 88.103 508.103 92.339
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
118 TPM2u+F 30.052 10 80.103 300.103 83.129
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
119 TPM2u+F+I 30.052 11 82.103 346.103 85.432
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
120 TPM2u+F+G4 30.053 11 82.105 346.105 85.434
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
121 TPM2u+F+I+G4 30.104 12 84.208 396.208 87.839
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
122 TPM2u+F+R2 30.052 12 84.103 396.103 87.734
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
123 TPM2u+F+R3 30.052 14 88.103 508.103 92.339
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
131 TPM3+F 30.187 10 80.375 300.375 83.401
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
132 TPM3+F+I 30.186 11 82.371 346.371 85.699
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
133 TPM3+F+G4 30.187 11 82.373 346.373 85.702
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
134 TPM3+F+I+G4 30.222 12 84.444 396.444 88.075
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
135 TPM3+F+R2 30.186 12 84.371 396.371 88.002
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
136 TPM3+F+R3 30.186 14 88.371 508.371 92.607
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
144 TPM3u+F 30.186 10 80.371 300.371 83.397
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
145 TPM3u+F+I 30.186 11 82.371 346.371 85.699
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
146 TPM3u+F+G4 30.187 11 82.373 346.373 85.702
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
147 TPM3u+F+I+G4 30.215 12 84.430 396.430 88.061
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
148 TPM3u+F+R2 30.186 12 84.371 396.371 88.002
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
149 TPM3u+F+R3 30.186 14 88.371 508.371 92.607
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
157 TIMe 30.756 8 77.512 221.512 79.933
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
158 TIMe+I 30.726 9 79.452 259.452 82.175
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
159 TIMe+G4 30.726 9 79.452 259.452 82.175
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
160 TIMe+I+G4 30.745 10 81.490 301.490 84.516
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
161 TIMe+R2 30.725 10 81.450 301.450 84.476
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
162 TIMe+R3 30.725 12 85.450 397.450 89.081
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
170 TIM+F 30.100 11 82.201 346.201 85.529
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
171 TIM+F+I 30.100 12 84.201 396.201 87.832
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
172 TIM+F+G4 30.101 12 84.203 396.203 87.834
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
173 TIM+F+I+G4 30.120 13 86.241 450.241 90.174
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
174 TIM+F+R2 30.100 13 86.201 450.201 90.134
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
175 TIM+F+R3 30.100 15 90.201 570.201 94.739
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
183 TIM2e 30.753 8 77.505 221.505 79.926
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
184 TIM2e+I 30.715 9 79.430 259.430 82.153
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
185 TIM2e+G4 30.715 9 79.430 259.430 82.153
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
186 TIM2e+I+G4 30.729 10 81.457 301.457 84.483
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
187 TIM2e+R2 30.714 10 81.428 301.428 84.454
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
188 TIM2e+R3 30.714 12 85.428 397.428 89.059
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
196 TIM2+F 30.052 11 82.104 346.104 85.433
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
197 TIM2+F+I 30.052 12 84.103 396.103 87.734
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
198 TIM2+F+G4 30.053 12 84.105 396.105 87.736
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
199 TIM2+F+I+G4 30.067 13 86.133 450.133 90.067
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
200 TIM2+F+R2 30.052 13 86.103 450.103 90.037
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
201 TIM2+F+R3 30.052 15 90.103 570.103 94.642
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
209 TIM3e 30.780 8 77.560 221.560 79.980
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
210 TIM3e+I 30.773 9 79.546 259.546 82.269
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
211 TIM3e+G4 30.773 9 79.546 259.546 82.270
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
212 TIM3e+I+G4 30.781 10 81.562 301.562 84.588
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
213 TIM3e+R2 30.772 10 81.545 301.545 84.570
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
214 TIM3e+R3 30.772 12 85.545 397.545 89.176
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
222 TIM3+F 30.186 11 82.371 346.371 85.699
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
223 TIM3+F+I 30.186 12 84.371 396.371 88.002
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
224 TIM3+F+G4 30.187 12 84.373 396.373 88.004
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
225 TIM3+F+I+G4 30.195 13 86.389 450.389 90.323
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
226 TIM3+F+R2 30.186 13 86.371 450.371 90.305
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
227 TIM3+F+R3 30.186 15 90.371 570.371 94.910
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
235 TVMe 30.609 9 79.217 259.217 81.941
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
236 TVMe+I 30.587 10 81.173 301.173 84.199
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
237 TVMe+G4 30.573 10 81.146 301.146 84.172
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
238 TVMe+I+G4 30.578 11 83.156 347.156 86.485
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
239 TVMe+R2 30.571 11 83.143 347.143 86.471
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
240 TVMe+R3 30.571 13 87.143 451.143 91.076
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
248 TVM+F 29.941 12 83.882 395.882 87.513
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
249 TVM+F+I 29.941 13 85.882 449.882 89.816
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
250 TVM+F+G4 29.942 13 85.885 449.885 89.818
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
251 TVM+F+I+G4 29.948 14 87.897 507.897 92.133
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
252 TVM+F+R2 29.941 14 87.882 507.882 92.119
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
253 TVM+F+R3 29.941 16 91.882 635.882 96.724
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
261 SYM 30.571 10 81.143 301.143 84.169
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
262 SYM+I 30.571 11 83.142 347.142 86.471
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
263 SYM+G4 30.572 11 83.144 347.144 86.473
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
264 SYM+I+G4 30.576 12 85.152 397.152 88.783
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
265 SYM+R2 30.571 12 85.142 397.142 88.773
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
266 SYM+R3 30.571 14 89.142 509.142 93.379
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
274 GTR+F 29.941 13 85.883 449.883 89.816
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
275 GTR+F+I 29.941 14 87.882 507.882 92.118
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
276 GTR+F+G4 29.942 14 87.884 507.884 92.121
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
277 GTR+F+I+G4 29.946 15 89.892 569.892 94.431
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
278 GTR+F+R2 29.941 15 89.882 569.882 94.421
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
279 GTR+F+R3 29.941 17 93.882 705.882 99.026
Akaike Information Criterion: K2P
Corrected Akaike Information Criterion: JC
Bayesian Information Criterion: K2P
Best-fit model: K2P chosen according to BIC

All model information printed to test.fasta.model.gz
CPU time for ModelFinder: 0.157 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.098 seconds (0h:0m:0s)

NOTE: 0 MB RAM (0 GB) is required!
WARNING: Number of threads seems too high for short alignments. Use -nt AUTO to determine best number of threads.
Estimate model parameters (epsilon = 0.100)

  1. Initial log-likelihood: -32.618
  2. Current log-likelihood: -30.840
    Optimal log-likelihood: -30.837
    Rate parameters: A-C: 1.00000 A-G: 0.00010 A-T: 1.00000 C-G: 1.00000 C-T: 0.00010 G-T: 1.00000
    Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
    Parameters optimization took 2 rounds (0.001 sec)
    Computing ML distances based on estimated model parameters... 0.001 sec
    Computing BIONJ tree...
    0.000 seconds
    Log-likelihood of BIONJ tree: -30.837

| INITIALIZING CANDIDATE TREE SET |

Generating 99 parsimony trees... 0.007 second
Computing log-likelihood of 2 initial trees ... 0.000 seconds
Current best score: -30.837

Do NNI search on 3 best initial trees
UPDATE BEST LOG-LIKELIHOOD: -30.837
Finish initializing candidate tree set (3)
Current best tree score: -30.837 / CPU time: 0.009
Number of iterations: 3

| OPTIMIZING CANDIDATE TREE SET |

UPDATE BEST LOG-LIKELIHOOD: -30.837
Iteration 10 / LogL: -30.839 / Time: 0h:0m:0s
UPDATE BEST LOG-LIKELIHOOD: -30.837
Iteration 20 / LogL: -30.839 / Time: 0h:0m:0s
Iteration 30 / LogL: -30.837 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 40 / LogL: -30.837 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 50 / LogL: -30.837 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 60 / LogL: -30.837 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 70 / LogL: -30.839 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 80 / LogL: -30.839 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 90 / LogL: -30.837 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 100 / LogL: -30.837 / Time: 0h:0m:0s (0h:0m:0s left)
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:0s

| FINALIZING TREE SEARCH |

Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)

  1. Initial log-likelihood: -30.837
    Optimal log-likelihood: -30.837
    Rate parameters: A-C: 1.00000 A-G: 0.00010 A-T: 1.00000 C-G: 1.00000 C-T: 0.00010 G-T: 1.00000
    Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
    Parameters optimization took 1 rounds (0.000 sec)
    BEST SCORE FOUND : -30.837
    Total tree length: 0.552

Total number of iterations: 101
CPU time used for tree search: 0.069 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.036 sec (0h:0m:0s)
Total CPU time used: 0.084 sec (0h:0m:0s)
Total wall-clock time used: 0.045 sec (0h:0m:0s)

Reading trees in no_br.trees ...
2 trees detected
Note: 0.061 MB of RAM required!
Creating 1000 bootstrap replicates...
done
Tree 1 / LogL: -30.837
Tree 2 / LogL: -34.343
Performing RELL-BP test...
Performing KH and SH test...
Performing ELW test...
Performing approximately unbiased (AU) test...
WARNING: Too few replicates for AU test. At least -zb 10000 for reliable results!
0 MB required for AU test
Generating 10 x 1000 multiscale bootstrap replicates... ERROR: STACK TRACE FOR
ERROR: DEBUGGING:* IQ-TRE CRA
ERROR: SHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: test.fasta.log
ERROR: *** Alignment files (if possible)

Alignment (test.fasta):

>A
ATTGTCCCGA
>B
ATGGTCCCCA
>C
TTTTTACCGA
>D
TTTGTACCGA

Trees (no_br.tre):

(A,B,(C,D));
(A,C,(B,D));
@CarlosSantanaMolina
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CarlosSantanaMolina commented Aug 2, 2018 •
edited
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Concernign to AU test bug, thanks for share this info.
Following the instrucctions in IQ-tree webpage (http://www.iqtree.org/doc/Advanced-Tutorial), I also had problems performing the AU topology-test with next warnings:

"""
WARNING: Too few replicates for AU test. At least -zb 10000 for reliable results!
0 MB required for AU test
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >'
Generating 10 x 1000 multiscale bootstrap replicates... ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 1 funcAbort()
ERROR: 2 ()
ERROR: 3 gsignal()
ERROR: 4 abort()
ERROR: 5 __gnu_cxx::__verbose_terminate_handler()
ERROR: 6 ()
ERROR: 7 ()
ERROR: 8 __gxx_personality_v0()
ERROR: 9 ()
ERROR: 10 _Unwind_Resume()
ERROR: 11 Alignment::createBootstrapAlignment(int*, char const*, int*)
ERROR: 13 GOMP_parallel()
ERROR: 14 performAUTest(Params&, PhyloTree*, double*, std::vector<TreeInfo, std::allocator >&)
ERROR: 15 evaluateTrees(Params&, IQTree*, std::vector<TreeInfo, std::allocator >&, std::vector<int, std::allocator >&)
ERROR: 16 reportPhyloAnalysis(Params&, IQTree&, ModelCheckpoint&)
ERROR: 17 runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 18 main()
ERROR: 19 __libc_start_main()
ERROR: 20 _start()
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: example.phy.log
ERROR: *** Alignment files (if possible)
Aborted (degenerated `core' )

"""

As Kinggerm said, with 6.1 version it works perfectly.
Cheers,
Carlos

@bqminh
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bqminh commented Aug 23, 2018 via email

@bqminh bqminh closed this as completed Sep 8, 2018
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