partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile

@@ -0,0 +1 @@
+(XnaiveX:0.0000010000,13de8675ec:0.0000010000,(((((20a0129b57:0.0027294000,97366cf0d8:0.0027294000)Node6:0.0000010000,33aaa62e12:0.0000010000)Node5:0.0000010000,31e052ee14:0.0000010000)Node4:0.0000010000,91796617a0:0.0000010000)Node3:0.0000010000,4233d708fe:0.0000010000)Node2:0.0000010000)Node1;

test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa

@@ -0,0 +1,16 @@
+>XnaiveX
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>162cb1691f
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG
+>17f57acf2e
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>73431a9b10
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>73d6c6e558
+CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>948b83fb4d
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>bf50fa2017
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>c8a90cc3d7
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG

test/ref-results/partition-new-simu/iqtree/iclust-2/log

@@ -0,0 +1,375 @@
+run /home/runner/work/partis/partis/bin/iqtree-3-linux -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out -o XnaiveX
+IQ-TREE version 3.0.1 for Linux x86 64-bit built May  5 2025
+Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
+Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow,
+Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt
+
+Host:    pkrvmubgrv54qmi (AVX2, FMA3, 15 GB RAM)
+Command: /home/runner/work/partis/partis/bin/iqtree3_intel -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out -o XnaiveX
+Seed:    801199 (Using SPRNG - Scalable Parallel Random Number Generator)
+Time:    Mon Aug 18 15:31:52 2025
+Kernel:  AVX+FMA - 1 threads (4 CPU cores detected)
+
+HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
+HINT: -nt AUTO will automatically determine the best number of threads to use.
+
+Reading alignment file /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa ... Fasta format detected
+Reading fasta file: done in 7.8927e-05 secs using 98.83% CPU
+Alignment most likely contains DNA/RNA sequences
+Constructing alignment: done in 0.000400938 secs using 36.17% CPU
+Alignment has 8 sequences with 379 columns, 21 distinct patterns
+4 parsimony-informative, 17 singleton sites, 358 constant sites
+            Gap/Ambiguity  Composition  p-value
+Analyzing sequences: done in 8.516e-06 secs
+   1  XnaiveX       0.00%    passed     99.90%
+   2  162cb1691f    0.00%    passed     99.94%
+   3  17f57acf2e    0.00%    passed     99.94%
+   4  73431a9b10    0.00%    passed     99.81%
+   5  73d6c6e558    0.00%    passed     98.68%
+   6  948b83fb4d    0.00%    passed     99.88%
+   7  bf50fa2017    0.00%    passed     99.81%
+   8  c8a90cc3d7    0.00%    passed     99.56%
+****  TOTAL         0.00%  0 sequences failed composition chi2 test (p-value<5%; df=3)
+
+
+Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
+Perform fast likelihood tree search using GTR+I+G model...
+Estimate model parameters (epsilon = 5.000)
+Perform nearest neighbor interchange...
+Optimizing NNI: done in 0.000480928 secs using 93.36% CPU
+Estimate model parameters (epsilon = 1.000)
+1. Initial log-likelihood: -668.906
+Optimal log-likelihood: -668.900
+Rate parameters:  A-C: 0.58043  A-G: 0.19277  A-T: 0.25950  C-G: 0.74204  C-T: 1.19039  G-T: 1.00000
+Base frequencies:  A: 0.219  C: 0.280  G: 0.285  T: 0.216
+Proportion of invariable sites: 0.470
+Gamma shape alpha: 998.448
+Parameters optimization took 1 rounds (0.001 sec)
+Time for fast ML tree search: 0.004 seconds
+
+NOTE: ModelFinder requires 0 MB RAM!
+ModelFinder will test up to 968 DNA models (sample size: 379 epsilon: 0.100) ...
+ No. Model         -LnL         df  AIC          AICc         BIC
+  1  JC            674.481      13  1374.962     1375.959     1426.150
+  2  JC+I          674.481      14  1376.962     1378.116     1432.088
+  3  JC+G4         674.481      14  1376.963     1378.117     1432.088
+  4  JC+I+G4       674.940      15  1379.879     1381.201     1438.942
+  5  JC+R2         674.481      15  1378.963     1380.285     1438.026
+  6  JC+R3         674.481      17  1382.962     1384.658     1449.900
+ 14  JC+I+R2       674.942      16  1381.884     1383.386     1444.884
+ 15  JC+I+R3       674.935      18  1385.870     1387.770     1456.746
+ 23  JC            674.481      13  1374.962     1375.959     1426.150
+ 24  JC+I          674.481      14  1376.962     1378.116     1432.088
+ 25  JC+G4         674.481      14  1376.963     1378.117     1432.088
+ 45  F81           674.481      13  1374.962     1375.959     1426.150
+ 46  F81+I         674.481      14  1376.962     1378.116     1432.088
+ 47  F81+G4        674.481      14  1376.963     1378.117     1432.088
+ 67  F81+F         671.490      16  1374.980     1376.482     1437.980
+ 68  F81+F+I       671.490      17  1376.980     1378.675     1443.918
+ 69  F81+F+G4      671.490      17  1376.980     1378.676     1443.918
+ 89  K2P           674.481      14  1376.962     1378.116     1432.087
+ 90  K2P+I         674.481      15  1378.962     1380.284     1438.025
+ 91  K2P+G4        674.481      15  1378.963     1380.285     1438.026
+111  K2P           674.481      14  1376.962     1378.116     1432.087
+112  K2P+I         674.481      15  1378.962     1380.284     1438.025
+113  K2P+G4        674.481      15  1378.963     1380.285     1438.026
+133  HKY           674.481      14  1376.962     1378.116     1432.087
+134  HKY+I         674.481      15  1378.962     1380.284     1438.025
+135  HKY+G4        674.481      15  1378.963     1380.285     1438.026
+155  HKY+F         671.489      17  1376.977     1378.673     1443.916
+156  HKY+F+I       671.489      18  1378.977     1380.877     1449.853
+157  HKY+F+G4      671.489      18  1378.978     1380.878     1449.854
+177  TNe           672.458      15  1374.916     1376.238     1433.979
+178  TNe+I         672.458      16  1376.916     1378.419     1439.917
+179  TNe+G4        672.458      16  1376.917     1378.420     1439.917
+199  TNe           672.458      15  1374.916     1376.238     1433.979
+200  TNe+I         672.458      16  1376.916     1378.419     1439.917
+201  TNe+G4        672.458      16  1376.917     1378.420     1439.917
+221  TN            672.458      15  1374.916     1376.238     1433.979
+222  TN+I          672.458      16  1376.916     1378.419     1439.917
+223  TN+G4         672.458      16  1376.917     1378.420     1439.917
+243  TN+F          669.425      18  1374.851     1376.751     1445.726
+244  TN+F+I        669.425      19  1376.851     1378.968     1451.664
+245  TN+F+G4       669.426      19  1376.852     1378.969     1451.665
+265  K3P           674.338      15  1378.676     1379.998     1437.739
+266  K3P+I         674.338      16  1380.676     1382.179     1443.676
+267  K3P+G4        674.338      16  1380.677     1382.179     1443.677
+287  K3P           674.338      15  1378.676     1379.998     1437.739
+288  K3P+I         674.338      16  1380.676     1382.179     1443.676
+289  K3P+G4        674.338      16  1380.677     1382.179     1443.677
+309  K3Pu          674.338      15  1378.676     1379.998     1437.739
+310  K3Pu+I        674.338      16  1380.676     1382.179     1443.676
+311  K3Pu+G4       674.338      16  1380.677     1382.179     1443.677
+331  K3Pu+F        671.310      18  1378.621     1380.521     1449.496
+332  K3Pu+F+I      671.310      19  1380.620     1382.737     1455.433
+333  K3Pu+F+G4     671.311      19  1380.621     1382.738     1455.434
+353  TPM2          673.519      15  1377.038     1378.360     1436.101
+354  TPM2+I        673.519      16  1379.038     1380.541     1442.039
+355  TPM2+G4       673.519      16  1379.039     1380.542     1442.039
+375  TPM2          673.519      15  1377.038     1378.360     1436.101
+376  TPM2+I        673.519      16  1379.038     1380.541     1442.039
+377  TPM2+G4       673.519      16  1379.039     1380.542     1442.039
+397  TPM2u         673.519      15  1377.038     1378.360     1436.101
+398  TPM2u+I       673.519      16  1379.038     1380.541     1442.038
+399  TPM2u+G4      673.519      16  1379.039     1380.542     1442.039
+419  TPM2u+F       670.831      18  1377.663     1379.563     1448.539
+420  TPM2u+F+I     670.831      19  1379.663     1381.780     1454.476
+421  TPM2u+F+G4    670.832      19  1379.664     1381.781     1454.477
+441  TPM3          674.438      15  1378.877     1380.199     1437.940
+442  TPM3+I        674.438      16  1380.877     1382.379     1443.877
+443  TPM3+G4       674.439      16  1380.877     1382.380     1443.878
+463  TPM3          674.438      15  1378.877     1380.199     1437.940
+464  TPM3+I        674.438      16  1380.877     1382.379     1443.877
+465  TPM3+G4       674.439      16  1380.877     1382.380     1443.878
+485  TPM3u         674.438      15  1378.876     1380.199     1437.940
+486  TPM3u+I       674.438      16  1380.876     1382.379     1443.877
+487  TPM3u+G4      674.439      16  1380.877     1382.380     1443.878
+507  TPM3u+F       671.487      18  1378.975     1380.875     1449.851
+508  TPM3u+F+I     671.487      19  1380.975     1383.092     1455.788
+509  TPM3u+F+G4    671.488      19  1380.975     1383.092     1455.789
+529  TIMe          672.315      16  1376.630     1378.133     1439.630
+530  TIMe+I        672.315      17  1378.630     1380.325     1445.568
+531  TIMe+G4       672.315      17  1378.631     1380.326     1445.569
+551  TIMe          672.315      16  1376.630     1378.133     1439.630
+552  TIMe+I        672.315      17  1378.630     1380.325     1445.568
+553  TIMe+G4       672.315      17  1378.631     1380.326     1445.569
+573  TIM           672.315      16  1376.630     1378.133     1439.630
+574  TIM+I         672.315      17  1378.630     1380.325     1445.568
+575  TIM+G4        672.315      17  1378.631     1380.326     1445.569
+595  TIM+F         669.247      19  1376.494     1378.611     1451.307
+596  TIM+F+I       669.247      20  1378.494     1380.840     1457.245
+597  TIM+F+G4      669.247      20  1378.495     1380.841     1457.246
+617  TIM2e         671.494      16  1374.988     1376.491     1437.988
+618  TIM2e+I       671.494      17  1376.988     1378.683     1443.926
+619  TIM2e+G4      671.494      17  1376.989     1378.684     1443.927
+639  TIM2e         671.494      16  1374.988     1376.491     1437.988
+640  TIM2e+I       671.494      17  1376.988     1378.683     1443.926
+641  TIM2e+G4      671.494      17  1376.989     1378.684     1443.927
+661  TIM2          671.494      16  1374.988     1376.491     1437.988
+662  TIM2+I        671.494      17  1376.988     1378.683     1443.926
+663  TIM2+G4       671.494      17  1376.989     1378.684     1443.927
+683  TIM2+F        668.767      19  1375.534     1377.651     1450.348
+684  TIM2+F+I      668.767      20  1377.534     1379.881     1456.285
+685  TIM2+F+G4     668.768      20  1377.535     1379.882     1456.286
+705  TIM3e         672.415      16  1376.831     1378.333     1439.831
+706  TIM3e+I       672.415      17  1378.831     1380.526     1445.769
+707  TIM3e+G4      672.416      17  1378.832     1380.527     1445.770
+727  TIM3e         672.415      16  1376.831     1378.333     1439.831
+728  TIM3e+I       672.415      17  1378.831     1380.526     1445.769
+729  TIM3e+G4      672.416      17  1378.832     1380.527     1445.770
+749  TIM3          672.415      16  1376.831     1378.333     1439.831
+750  TIM3+I        672.415      17  1378.831     1380.526     1445.769
+751  TIM3+G4       672.416      17  1378.832     1380.527     1445.770
+771  TIM3+F        669.424      19  1376.849     1378.966     1451.662
+772  TIM3+F+I      669.424      20  1378.849     1381.195     1457.599
+773  TIM3+F+G4     669.425      20  1378.850     1381.196     1457.600
+793  TVMe          673.109      17  1380.218     1381.914     1447.157
+794  TVMe+I        673.109      18  1382.218     1384.118     1453.094
+795  TVMe+G4       673.110      18  1382.219     1384.119     1453.095
+815  TVMe          673.109      17  1380.218     1381.914     1447.157
+816  TVMe+I        673.109      18  1382.218     1384.118     1453.094
+817  TVMe+G4       673.110      18  1382.219     1384.119     1453.095
+837  TVM           673.109      17  1380.218     1381.914     1447.156
+838  TVM+I         673.109      18  1382.218     1384.118     1453.094
+839  TVM+G4        673.109      18  1382.219     1384.119     1453.095
+859  TVM+F         670.452      20  1380.904     1383.251     1459.655
+860  TVM+F+I       670.452      21  1382.904     1385.493     1465.593
+861  TVM+F+G4      670.453      21  1382.905     1385.493     1465.593
+881  SYM           671.084      18  1378.168     1380.068     1449.043
+882  SYM+I         671.084      19  1380.168     1382.285     1454.981
+883  SYM+G4        671.084      19  1380.169     1382.286     1454.982
+903  SYM           671.084      18  1378.168     1380.068     1449.043
+904  SYM+I         671.084      19  1380.168     1382.285     1454.981
+905  SYM+G4        671.084      19  1380.169     1382.286     1454.982
+925  GTR           671.084      18  1378.168     1380.068     1449.043
+926  GTR+I         671.084      19  1380.168     1382.285     1454.981
+927  GTR+G4        671.084      19  1380.169     1382.286     1454.982
+947  GTR+F         668.388      21  1378.775     1381.363     1461.463
+948  GTR+F+I       668.388      22  1380.775     1383.618     1467.401
+949  GTR+F+G4      668.388      22  1380.776     1383.619     1467.402
+Akaike Information Criterion:           TN+F
+Corrected Akaike Information Criterion: JC
+Bayesian Information Criterion:         JC
+Best-fit model: JC chosen according to BIC
+
+All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz
+CPU time for ModelFinder: 0.066 seconds (0h:0m:0s)
+Wall-clock time for ModelFinder: 0.075 seconds (0h:0m:0s)
+
+NOTE: 0 MB RAM (0 GB) is required!
+Estimate model parameters (epsilon = 0.100)
+1. Initial log-likelihood: -674.481
+Optimal log-likelihood: -674.481
+Rate parameters:  A-C: 1.00000  A-G: 1.00000  A-T: 1.00000  C-G: 1.00000  C-T: 1.00000  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)
+Wrote distance file to... 
+Computing ML distances based on estimated model parameters...
+Calculating distance matrix: done in 0.000124302 secs using 89.3% CPU
+Computing ML distances took 0.000140 sec (of wall-clock time) 0.000127 sec (of CPU time)
+Setting up auxiliary I and S matrices: done in 2.667e-05 secs using 86.24% CPU
+Constructing RapidNJ tree: done in 3.232e-05 secs using 86.63% CPU
+Computing RapidNJ tree took 0.000079 sec (of wall-clock time) 0.000071 sec (of CPU time)
+Log-likelihood of RapidNJ tree: -680.247
+--------------------------------------------------------------------
+|             INITIALIZING CANDIDATE TREE SET                      |
+--------------------------------------------------------------------
+Generating 98 parsimony trees... 0.015 second
+Computing log-likelihood of 66 initial trees ... 0.005 seconds
+Current best score: -674.481
+
+Do NNI search on 20 best initial trees
+Optimizing NNI: done in 0.000217055 secs using 90.76% CPU
+Estimate model parameters (epsilon = 0.100)
+BETTER TREE FOUND at iteration 1: -674.481
+Optimizing NNI: done in 0.000177983 secs
+Optimizing NNI: done in 0.000207597 secs
+Optimizing NNI: done in 0.000200935 secs
+Optimizing NNI: done in 0.000228316 secs using 91.1% CPU
+Optimizing NNI: done in 0.000206866 secs using 89.91% CPU
+Optimizing NNI: done in 0.000225581 secs using 89.99% CPU
+Optimizing NNI: done in 0.000206025 secs using 90.28% CPU
+Optimizing NNI: done in 0.000223937 secs using 99.58% CPU
+Optimizing NNI: done in 0.000442726 secs using 99.84% CPU
+Iteration 10 / LogL: -674.481 / Time: 0h:0m:0s
+Optimizing NNI: done in 0.000450561 secs
+Optimizing NNI: done in 0.000436274 secs
+Optimizing NNI: done in 0.000435944 secs using 51.38% CPU
+Optimizing NNI: done in 0.000434852 secs using 99.8% CPU
+Optimizing NNI: done in 0.000196477 secs using 99.25% CPU
+Optimizing NNI: done in 0.000475437 secs using 99.7% CPU
+Optimizing NNI: done in 0.000667235 secs using 99.96% CPU
+Optimizing NNI: done in 0.000832193 secs using 99.86% CPU
+Optimizing NNI: done in 0.000882326 secs using 99.85% CPU
+Optimizing NNI: done in 0.000560486 secs using 99.91% CPU
+Iteration 20 / LogL: -674.482 / Time: 0h:0m:0s
+Finish initializing candidate tree set (5)
+Current best tree score: -674.481 / CPU time: 0.029
+Number of iterations: 20
+--------------------------------------------------------------------
+|               OPTIMIZING CANDIDATE TREE SET                      |
+--------------------------------------------------------------------
+Optimizing NNI: done in 0.000679819 secs using 99.73% CPU
+Optimizing NNI: done in 0.000644582 secs
+Optimizing NNI: done in 0.000658519 secs using 70.16% CPU
+Optimizing NNI: done in 0.000650203 secs using 99.81% CPU
+Optimizing NNI: done in 0.000673918 secs using 99.86% CPU
+UPDATE BEST LOG-LIKELIHOOD: -674.481
+Optimizing NNI: done in 0.00122079 secs using 99.94% CPU
+Optimizing NNI: done in 0.000625246 secs using 99.8% CPU
+Optimizing NNI: done in 0.000833606 secs using 99.93% CPU
+Optimizing NNI: done in 0.000204742 secs using 99.64% CPU
+Optimizing NNI: done in 0.000206194 secs using 99.42% CPU
+Iteration 30 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000249656 secs using 99.34% CPU
+Optimizing NNI: done in 0.000666033 secs using 99.84% CPU
+Optimizing NNI: done in 0.000633072 secs using 99.83% CPU
+Optimizing NNI: done in 0.000508219 secs
+Optimizing NNI: done in 0.000685609 secs using 45.8% CPU
+Optimizing NNI: done in 0.000708683 secs using 99.48% CPU
+Optimizing NNI: done in 0.000466461 secs using 99.9% CPU
+Optimizing NNI: done in 0.000424231 secs using 99.71% CPU
+Optimizing NNI: done in 0.000520872 secs using 99.64% CPU
+Optimizing NNI: done in 0.000988114 secs using 1.214% CPU
+Iteration 40 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000623232 secs using 99.8% CPU
+Optimizing NNI: done in 0.000663117 secs using 99.83% CPU
+Optimizing NNI: done in 0.00054122 secs using 99.77% CPU
+Optimizing NNI: done in 0.000631208 secs using 99.81% CPU
+Optimizing NNI: done in 0.00065394 secs using 99.86% CPU
+Optimizing NNI: done in 0.000645064 secs using 99.84% CPU
+Optimizing NNI: done in 0.000288789 secs using 98.34% CPU
+Optimizing NNI: done in 0.000603405 secs using 99.77% CPU
+Optimizing NNI: done in 0.000654271 secs
+Optimizing NNI: done in 0.000659972 secs using 81.82% CPU
+Iteration 50 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000421727 secs using 89.16% CPU
+Optimizing NNI: done in 0.000464126 secs using 99.76% CPU
+Optimizing NNI: done in 0.000668187 secs
+Optimizing NNI: done in 0.000209701 secs
+Optimizing NNI: done in 0.000208549 secs using 32.61% CPU
+Optimizing NNI: done in 0.000460509 secs using 99.89% CPU
+Optimizing NNI: done in 0.000645956 secs using 99.85% CPU
+Optimizing NNI: done in 0.000427648 secs using 99.85% CPU
+UPDATE BEST LOG-LIKELIHOOD: -674.481
+Optimizing NNI: done in 0.000517596 secs using 99.69% CPU
+Optimizing NNI: done in 0.000511264 secs using 99.56% CPU
+Iteration 60 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000703683 secs using 98.91% CPU
+Optimizing NNI: done in 0.000458335 secs using 99.71% CPU
+Optimizing NNI: done in 0.000451051 secs using 99.77% CPU
+Optimizing NNI: done in 0.000454178 secs using 99.74% CPU
+Optimizing NNI: done in 0.000536741 secs using 99.86% CPU
+Optimizing NNI: done in 0.00043974 secs using 99.83% CPU
+Optimizing NNI: done in 0.000646577 secs using 99.76% CPU
+Optimizing NNI: done in 0.000493791 secs using 99.84% CPU
+Optimizing NNI: done in 0.000204842 secs using 99.59% CPU
+Optimizing NNI: done in 0.000464186 secs
+Iteration 70 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00047201 secs
+Optimizing NNI: done in 0.00045498 secs using 98.47% CPU
+Optimizing NNI: done in 0.000373878 secs using 88.8% CPU
+Optimizing NNI: done in 0.000722138 secs using 99.84% CPU
+Optimizing NNI: done in 0.000205603 secs using 97.27% CPU
+Optimizing NNI: done in 0.00064866 secs using 99.9% CPU
+Optimizing NNI: done in 0.000501025 secs using 99.8% CPU
+Optimizing NNI: done in 0.000722497 secs using 99.79% CPU
+Optimizing NNI: done in 0.00043945 secs using 99.9% CPU
+Optimizing NNI: done in 0.000196998 secs using 99.49% CPU
+UPDATE BEST LOG-LIKELIHOOD: -674.481
+Iteration 80 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000201355 secs using 99.33% CPU
+Optimizing NNI: done in 0.000454559 secs using 99.66% CPU
+Optimizing NNI: done in 0.000518768 secs using 99.85% CPU
+Optimizing NNI: done in 0.000204713 secs using 99.16% CPU
+Optimizing NNI: done in 0.000481629 secs using 99.87% CPU
+Optimizing NNI: done in 0.000195625 secs using 99.68% CPU
+Optimizing NNI: done in 0.00043947 secs using 99.89% CPU
+UPDATE BEST LOG-LIKELIHOOD: -674.481
+Optimizing NNI: done in 0.000517165 secs using 99.77% CPU
+Optimizing NNI: done in 0.00049828 secs using 99.74% CPU
+Optimizing NNI: done in 0.000421847 secs using 99.8% CPU
+Iteration 90 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000205774 secs using 99.62% CPU
+Optimizing NNI: done in 0.000674708 secs
+Optimizing NNI: done in 0.000457274 secs
+Optimizing NNI: done in 0.000385929 secs using 99.76% CPU
+Optimizing NNI: done in 0.000474164 secs using 99.75% CPU
+Optimizing NNI: done in 0.000494753 secs using 99.65% CPU
+Optimizing NNI: done in 0.000419853 secs
+Optimizing NNI: done in 0.000715395 secs using 35.92% CPU
+Optimizing NNI: done in 0.000683946 secs using 99.57% CPU
+Optimizing NNI: done in 0.000729591 secs using 99.92% CPU
+Iteration 100 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00022019 secs using 99.46% CPU
+Optimizing NNI: done in 0.000455971 secs using 99.79% CPU
+TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
+
+--------------------------------------------------------------------
+|                    FINALIZING TREE SEARCH                        |
+--------------------------------------------------------------------
+Performs final model parameters optimization
+Estimate model parameters (epsilon = 0.010)
+1. Initial log-likelihood: -674.481
+Optimal log-likelihood: -674.481
+Rate parameters:  A-C: 1.00000  A-G: 1.00000  A-T: 1.00000  C-G: 1.00000  C-T: 1.00000  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 : -674.481
+Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
+Total tree length: 0.056
+
+Total number of iterations: 102
+CPU time used for tree search: 0.080 sec (0h:0m:0s)
+Wall-clock time used for tree search: 0.082 sec (0h:0m:0s)
+Total CPU time used: 0.154 sec (0h:0m:0s)
+Total wall-clock time used: 0.169 sec (0h:0m:0s)
+
+Analysis results written to: 
+  IQ-TREE report:                /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree
+  Maximum-likelihood tree:       /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile
+  Likelihood distances:          /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist
+  Ancestral state:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
+  Screen log file:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.log
+
+Date and Time: Mon Aug 18 15:31:52 2025

test/ref-results/partition-new-simu/iqtree/iclust-2/out.bionj

@@ -0,0 +1 @@
+((XnaiveX:0.0025902023,c8a90cc3d7:0.016110541):0.001381147,((162cb1691f:0.0053297933,17f57acf2e:0.002627736):0.0047392142,73d6c6e558:0.011337848):-0.0013482573,(948b83fb4d:0.0061970716,(73431a9b10:0.0053405152,bf50fa2017:-4.4832937e-05):0.001788862):0.0013337678);