Closed Kinggerm closed 5 years ago
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
"""
As Kinggerm said, with 6.1 version it works perfectly. Cheers, Carlos
Hi Carlos,
The AU test is temporarily disabled as it’s unclear how it resolves numerical issue when bp-rell are zero. We’ll need to investigate this carefully before offering the test again. Thanks for your understanding
Minh
On 2 Aug 2018, at 11:47 pm, CarlosSantanaMolina notifications@github.com wrote:
Concernign to AU test bug, thanks for share this info. Following the instrucctions in IQ-tree webpage (http://www.iqtree.org/doc/Advanced-Tutorial 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 work perfectly. Cheers, Carlos
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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)
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)
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):
Trees (no_br.tre):