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-0/out.log

@@ -0,0 +1,429 @@
+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-0/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out -o XnaiveX
+Seed:    769287 (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-0/input-seqs.fa ... Fasta format detected
+Reading fasta file: done in 0.000109043 secs using 65.11% CPU
+Alignment most likely contains DNA/RNA sequences
+Constructing alignment: done in 0.000357497 secs using 99.58% CPU
+WARNING: 6 sites contain only gaps or ambiguous characters.
+Alignment has 12 sequences with 352 columns, 29 distinct patterns
+8 parsimony-informative, 20 singleton sites, 324 constant sites
+            Gap/Ambiguity  Composition  p-value
+Analyzing sequences: done in 9.517e-06 secs using 84.06% CPU
+   1  XnaiveX       1.70%    passed     99.41%
+   2  18f4019708    1.70%    passed     99.75%
+   3  308de1d739    1.70%    passed     98.96%
+   4  5fb484a8a6    1.70%    passed     99.94%
+   5  648902c3e5    1.70%    passed     99.27%
+   6  8024ed1a22    1.70%    passed     99.27%
+   7  822801f8ab    1.70%    passed     99.41%
+   8  d024e5cab0    1.70%    passed     99.41%
+   9  ee25049b92    1.70%    passed     97.94%
+  10  efdea248af    1.70%    passed     99.57%
+  11  f47122f1f5    1.70%    passed     99.27%
+  12  9c3cedb840    1.70%    passed     99.78%
+****  TOTAL         1.70%  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 0.000540719 secs using 84.33% CPU
+Estimate model parameters (epsilon = 1.000)
+1. Initial log-likelihood: -663.729
+Optimal log-likelihood: -663.717
+Rate parameters:  A-C: 0.93502  A-G: 0.93475  A-T: 0.45115  C-G: 0.67930  C-T: 0.80175  G-T: 1.00000
+Base frequencies:  A: 0.222  C: 0.257  G: 0.308  T: 0.213
+Proportion of invariable sites: 0.455
+Gamma shape alpha: 998.447
+Parameters optimization took 1 rounds (0.001 sec)
+Time for fast ML tree search: 0.003 seconds
+
+NOTE: ModelFinder requires 0 MB RAM!
+ModelFinder will test up to 968 DNA models (sample size: 352 epsilon: 0.100) ...
+ No. Model         -LnL         df  AIC          AICc         BIC
+  1  JC            667.319      21  1376.639     1379.439     1457.775
+  2  JC+I          667.319      22  1378.639     1381.715     1463.639
+  3  JC+G4         667.320      22  1378.641     1381.717     1463.640
+  4  JC+I+G4       668.194      23  1382.388     1385.753     1471.251
+  5  JC+R2         667.320      23  1380.640     1384.006     1469.503
+  6  JC+R3         667.320      25  1384.639     1388.627     1481.230
+ 14  JC+I+R2       668.203      24  1384.405     1388.075     1477.133
+ 15  JC+I+R3       668.176      26  1388.352     1392.672     1488.806
+ 23  JC            667.319      21  1376.639     1379.439     1457.775
+ 24  JC+I          667.319      22  1378.639     1381.715     1463.639
+ 25  JC+G4         667.320      22  1378.641     1381.717     1463.640
+ 45  F81           667.320      21  1376.639     1379.439     1457.775
+ 46  F81+I         667.320      22  1378.639     1381.715     1463.639
+ 47  F81+G4        667.320      22  1378.641     1381.717     1463.641
+ 67  F81+F         663.546      24  1375.093     1378.763     1467.820
+ 68  F81+F+I       663.546      25  1377.093     1381.081     1473.684
+ 69  F81+F+G4      663.547      25  1377.095     1381.082     1473.685
+ 89  K2P           667.283      22  1378.566     1381.642     1463.566
+ 90  K2P+I         667.283      23  1380.566     1383.932     1469.430
+ 91  K2P+G4        667.284      23  1380.568     1383.934     1469.431
+111  K2P           667.283      22  1378.566     1381.642     1463.566
+112  K2P+I         667.283      23  1380.566     1383.932     1469.430
+113  K2P+G4        667.284      23  1380.568     1383.934     1469.431
+133  HKY           667.283      22  1378.566     1381.642     1463.566
+134  HKY+I         667.283      23  1380.566     1383.932     1469.430
+135  HKY+G4        667.284      23  1380.568     1383.934     1469.431
+155  HKY+F         663.502      25  1377.004     1380.992     1473.595
+156  HKY+F+I       663.502      26  1379.004     1383.324     1479.458
+157  HKY+F+G4      663.503      26  1379.006     1383.326     1479.460
+177  TNe           667.185      23  1380.371     1383.737     1469.234
+178  TNe+I         667.185      24  1382.371     1386.041     1475.098
+179  TNe+G4        667.186      24  1382.373     1386.042     1475.100
+199  TNe           667.185      23  1380.371     1383.737     1469.234
+200  TNe+I         667.185      24  1382.371     1386.041     1475.098
+201  TNe+G4        667.186      24  1382.373     1386.042     1475.100
+221  TN            667.185      23  1380.371     1383.737     1469.234
+222  TN+I          667.185      24  1382.371     1386.041     1475.098
+223  TN+G4         667.186      24  1382.373     1386.042     1475.100
+243  TN+F          663.461      26  1378.923     1383.243     1479.377
+244  TN+F+I        663.461      27  1380.923     1385.589     1485.241
+245  TN+F+G4       663.462      27  1380.924     1385.591     1485.242
+265  K3P           666.838      23  1379.676     1383.042     1468.539
+266  K3P+I         666.838      24  1381.676     1385.345     1474.403
+267  K3P+G4        666.839      24  1381.677     1385.347     1474.405
+287  K3P           666.838      23  1379.676     1383.042     1468.539
+288  K3P+I         666.838      24  1381.676     1385.345     1474.403
+289  K3P+G4        666.839      24  1381.677     1385.347     1474.405
+309  K3Pu          666.838      23  1379.676     1383.041     1468.539
+310  K3Pu+I        666.838      24  1381.676     1385.345     1474.403
+311  K3Pu+G4       666.839      24  1381.677     1385.347     1474.404
+331  K3Pu+F        662.995      26  1377.990     1382.310     1478.445
+332  K3Pu+F+I      662.995      27  1379.990     1384.657     1484.308
+333  K3Pu+F+G4     662.996      27  1379.992     1384.658     1484.310
+353  TPM2          667.114      23  1380.228     1383.594     1469.092
+354  TPM2+I        667.114      24  1382.228     1385.898     1474.955
+355  TPM2+G4       667.115      24  1382.230     1385.900     1474.957
+375  TPM2          667.114      23  1380.228     1383.594     1469.092
+376  TPM2+I        667.114      24  1382.228     1385.898     1474.955
+377  TPM2+G4       667.115      24  1382.230     1385.900     1474.957
+397  TPM2u         667.114      23  1380.228     1383.594     1469.092
+398  TPM2u+I       667.114      24  1382.228     1385.898     1474.955
+399  TPM2u+G4      667.115      24  1382.230     1385.900     1474.957
+419  TPM2u+F       663.468      26  1378.936     1383.256     1479.391
+420  TPM2u+F+I     663.468      27  1380.936     1385.603     1485.254
+421  TPM2u+F+G4    663.469      27  1380.938     1385.604     1485.256
+441  TPM3          667.241      23  1380.482     1383.848     1469.346
+442  TPM3+I        667.241      24  1382.482     1386.152     1475.209
+443  TPM3+G4       667.242      24  1382.484     1386.154     1475.211
+463  TPM3          667.241      23  1380.482     1383.848     1469.346
+464  TPM3+I        667.241      24  1382.482     1386.152     1475.209
+465  TPM3+G4       667.242      24  1382.484     1386.154     1475.211
+485  TPM3u         667.241      23  1380.482     1383.848     1469.346
+486  TPM3u+I       667.241      24  1382.482     1386.152     1475.209
+487  TPM3u+G4      667.242      24  1382.484     1386.154     1475.211
+507  TPM3u+F       663.499      26  1378.998     1383.318     1479.452
+508  TPM3u+F+I     663.499      27  1380.998     1385.664     1485.316
+509  TPM3u+F+G4    663.500      27  1380.999     1385.666     1485.317
+529  TIMe          666.740      24  1381.481     1385.150     1474.208
+530  TIMe+I        666.740      25  1383.480     1387.468     1480.071
+531  TIMe+G4       666.741      25  1383.482     1387.470     1480.073
+551  TIMe          666.740      24  1381.481     1385.150     1474.208
+552  TIMe+I        666.740      25  1383.480     1387.468     1480.071
+553  TIMe+G4       666.741      25  1383.482     1387.470     1480.073
+573  TIM           666.740      24  1381.480     1385.150     1474.208
+574  TIM+I         666.740      25  1383.480     1387.468     1480.071
+575  TIM+G4        666.741      25  1383.482     1387.470     1480.073
+595  TIM+F         662.954      27  1379.909     1384.575     1484.227
+596  TIM+F+I       662.954      28  1381.909     1386.937     1490.090
+597  TIM+F+G4      662.955      28  1381.910     1386.938     1490.092
+617  TIM2e         667.017      24  1382.033     1385.703     1474.760
+618  TIM2e+I       667.017      25  1384.033     1388.021     1480.624
+619  TIM2e+G4      667.017      25  1384.035     1388.023     1480.626
+639  TIM2e         667.017      24  1382.033     1385.703     1474.760
+640  TIM2e+I       667.017      25  1384.033     1388.021     1480.624
+641  TIM2e+G4      667.017      25  1384.035     1388.023     1480.626
+661  TIM2          667.017      24  1382.033     1385.703     1474.760
+662  TIM2+I        667.017      25  1384.033     1388.021     1480.624
+663  TIM2+G4       667.017      25  1384.035     1388.023     1480.626
+683  TIM2+F        663.427      27  1380.854     1385.521     1485.172
+684  TIM2+F+I      663.427      28  1382.854     1387.882     1491.036
+685  TIM2+F+G4     663.428      28  1382.856     1387.884     1491.037
+705  TIM3e         667.144      24  1382.287     1385.957     1475.014
+706  TIM3e+I       667.144      25  1384.287     1388.275     1480.878
+707  TIM3e+G4      667.144      25  1384.289     1388.276     1480.879
+727  TIM3e         667.144      24  1382.287     1385.957     1475.014
+728  TIM3e+I       667.144      25  1384.287     1388.275     1480.878
+729  TIM3e+G4      667.144      25  1384.289     1388.276     1480.879
+749  TIM3          667.144      24  1382.287     1385.957     1475.014
+750  TIM3+I        667.143      25  1384.287     1388.275     1480.878
+751  TIM3+G4       667.144      25  1384.289     1388.276     1480.879
+771  TIM3+F        663.458      27  1380.916     1385.583     1485.234
+772  TIM3+F+I      663.458      28  1382.916     1387.944     1491.098
+773  TIM3+F+G4     663.459      28  1382.918     1387.946     1491.099
+793  TVMe          666.493      25  1382.987     1386.975     1479.578
+794  TVMe+I        666.493      26  1384.987     1389.307     1485.441
+795  TVMe+G4       666.494      26  1384.988     1389.308     1485.443
+815  TVMe          666.493      25  1382.987     1386.975     1479.578
+816  TVMe+I        666.493      26  1384.987     1389.307     1485.441
+817  TVMe+G4       666.494      26  1384.988     1389.308     1485.443
+837  TVM           666.493      25  1382.987     1386.975     1479.578
+838  TVM+I         666.493      26  1384.987     1389.307     1485.441
+839  TVM+G4        666.494      26  1384.988     1389.308     1485.443
+859  TVM+F         662.870      28  1381.740     1386.768     1489.922
+860  TVM+F+I       662.870      29  1383.740     1389.144     1495.786
+861  TVM+F+G4      662.871      29  1383.742     1389.146     1495.787
+881  SYM           666.396      26  1384.793     1389.113     1485.247
+882  SYM+I         666.396      27  1386.793     1391.459     1491.111
+883  SYM+G4        666.397      27  1386.794     1391.461     1491.113
+903  SYM           666.396      26  1384.793     1389.113     1485.247
+904  SYM+I         666.396      27  1386.793     1391.459     1491.111
+905  SYM+G4        666.397      27  1386.794     1391.461     1491.113
+925  GTR           666.396      26  1384.792     1389.112     1485.247
+926  GTR+I         666.396      27  1386.792     1391.459     1491.110
+927  GTR+G4        666.397      27  1386.794     1391.461     1491.112
+947  GTR+F         662.829      29  1383.659     1389.062     1495.704
+948  GTR+F+I       662.829      30  1385.659     1391.453     1501.568
+949  GTR+F+G4      662.830      30  1385.660     1391.455     1501.569
+Akaike Information Criterion:           F81+F
+Corrected Akaike Information Criterion: F81+F
+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-0/out.model.gz
+CPU time for ModelFinder: 0.121 seconds (0h:0m:0s)
+Wall-clock time for ModelFinder: 0.131 seconds (0h:0m:0s)
+
+NOTE: 0 MB RAM (0 GB) is required!
+Estimate model parameters (epsilon = 0.100)
+1. Initial log-likelihood: -667.320
+Optimal log-likelihood: -667.320
+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 0.000403323 secs using 98.68% CPU
+Computing ML distances took 0.000429 sec (of wall-clock time) 0.000428 sec (of CPU time)
+Setting up auxiliary I and S matrices: done in 3.3001e-05 secs using 96.97% CPU
+Constructing RapidNJ tree: done in 5.6235e-05 secs using 97.8% CPU
+Computing RapidNJ tree took 0.000111 sec (of wall-clock time) 0.000111 sec (of CPU time)
+Log-likelihood of RapidNJ tree: -667.322
+--------------------------------------------------------------------
+|             INITIALIZING CANDIDATE TREE SET                      |
+--------------------------------------------------------------------
+Generating 98 parsimony trees... 0.023 second
+Computing log-likelihood of 98 initial trees ... 0.021 seconds
+Current best score: -667.319
+
+Do NNI search on 20 best initial trees
+Optimizing NNI: done in 0.000583208 secs using 99.79% CPU
+Estimate model parameters (epsilon = 0.100)
+BETTER TREE FOUND at iteration 1: -667.319
+Optimizing NNI: done in 0.00058908 secs using 99.65% CPU
+Optimizing NNI: done in 0.000594609 secs using 99.73% CPU
+Optimizing NNI: done in 0.000607925 secs using 99.68% CPU
+Optimizing NNI: done in 0.000597635 secs using 99.73% CPU
+Optimizing NNI: done in 0.000564944 secs using 99.83% CPU
+Optimizing NNI: done in 0.000588819 secs using 99.86% CPU
+Optimizing NNI: done in 0.00055219 secs using 99.78% CPU
+Optimizing NNI: done in 0.000561248 secs using 99.78% CPU
+Optimizing NNI: done in 0.000552591 secs using 99.71% CPU
+Iteration 10 / LogL: -667.319 / Time: 0h:0m:0s
+Optimizing NNI: done in 0.000575605 secs
+Optimizing NNI: done in 0.000551479 secs using 50.95% CPU
+Optimizing NNI: done in 0.000585352 secs using 99.77% CPU
+Optimizing NNI: done in 0.000569011 secs using 99.82% CPU
+Optimizing NNI: done in 0.000559384 secs using 99.75% CPU
+Optimizing NNI: done in 0.000576917 secs using 99.67% CPU
+Optimizing NNI: done in 0.000569773 secs using 99.69% CPU
+Optimizing NNI: done in 0.000561728 secs using 99.87% CPU
+Optimizing NNI: done in 0.000567829 secs using 99.68% CPU
+Optimizing NNI: done in 0.000548704 secs using 99.87% CPU
+Iteration 20 / LogL: -667.319 / Time: 0h:0m:0s
+Finish initializing candidate tree set (20)
+Current best tree score: -667.319 / CPU time: 0.059
+Number of iterations: 20
+--------------------------------------------------------------------
+|               OPTIMIZING CANDIDATE TREE SET                      |
+--------------------------------------------------------------------
+Optimizing NNI: done in 0.00195848 secs using 75.11% CPU
+Optimizing NNI: done in 0.00184058 secs using 99.97% CPU
+Optimizing NNI: done in 0.00124317 secs using 99.91% CPU
+Optimizing NNI: done in 0.00102045 secs using 1.568% CPU
+Optimizing NNI: done in 0.00206472 secs using 99.92% CPU
+Optimizing NNI: done in 0.00116884 secs using 99.93% CPU
+Optimizing NNI: done in 0.00120539 secs using 99.88% CPU
+Optimizing NNI: done in 0.00116312 secs using 99.9% CPU
+Optimizing NNI: done in 0.0013657 secs using 99.95% CPU
+Optimizing NNI: done in 0.00120381 secs using 99.93% CPU
+Iteration 30 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00163443 secs using 98.99% CPU
+Optimizing NNI: done in 0.000440923 secs using 99.56% CPU
+Optimizing NNI: done in 0.000354081 secs using 99.69% CPU
+Optimizing NNI: done in 0.000392342 secs using 99.66% CPU
+Optimizing NNI: done in 0.000735252 secs using 99.83% CPU
+Optimizing NNI: done in 0.000724742 secs
+BETTER TREE FOUND at iteration 36: -667.319
+Optimizing NNI: done in 0.000843564 secs using 59.51% CPU
+Optimizing NNI: done in 0.000363658 secs using 99.82% CPU
+UPDATE BEST LOG-LIKELIHOOD: -667.319
+Optimizing NNI: done in 0.00102759 secs
+Optimizing NNI: done in 0.000350463 secs
+Iteration 40 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000909116 secs using 99.77% CPU
+Optimizing NNI: done in 0.000884531 secs
+Optimizing NNI: done in 0.000752103 secs using 99.85% CPU
+Optimizing NNI: done in 0.000808028 secs using 99.87% CPU
+Optimizing NNI: done in 0.00093791 secs using 99.9% CPU
+Optimizing NNI: done in 0.00133528 secs using 99.9% CPU
+Optimizing NNI: done in 0.0008036 secs using 99.93% CPU
+Optimizing NNI: done in 0.000281736 secs using 99.74% CPU
+BETTER TREE FOUND at iteration 48: -667.319
+Optimizing NNI: done in 0.000925968 secs
+Optimizing NNI: done in 0.00109964 secs using 94.49% CPU
+Iteration 50 / LogL: -687.190 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00153726 secs using 99.92% CPU
+Optimizing NNI: done in 0.00123191 secs using 99.93% CPU
+Optimizing NNI: done in 0.00168443 secs using 44.47% CPU
+Optimizing NNI: done in 0.000368046 secs using 92.65% CPU
+Optimizing NNI: done in 0.000743046 secs using 99.86% CPU
+Optimizing NNI: done in 0.0015048 secs using 15.22% CPU
+Optimizing NNI: done in 0.000851769 secs
+Optimizing NNI: done in 0.000348871 secs
+Optimizing NNI: done in 0.000820511 secs using 93.48% CPU
+Optimizing NNI: done in 0.00121983 secs using 99.93% CPU
+Iteration 60 / LogL: -667.321 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000360823 secs using 99.77% CPU
+Optimizing NNI: done in 0.000878509 secs using 99.83% CPU
+Optimizing NNI: done in 0.000795814 secs using 99.9% CPU
+Optimizing NNI: done in 0.00127491 secs using 99.07% CPU
+Optimizing NNI: done in 0.000361325 secs using 99.63% CPU
+Optimizing NNI: done in 0.000816143 secs using 99.86% CPU
+Optimizing NNI: done in 0.000805203 secs using 99.85% CPU
+Optimizing NNI: done in 0.00136598 secs using 99.86% CPU
+Optimizing NNI: done in 0.000345034 secs using 99.7% CPU
+Optimizing NNI: done in 0.000383516 secs using 99.6% CPU
+Iteration 70 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000344934 secs using 99.73% CPU
+Optimizing NNI: done in 0.000798119 secs using 99.86% CPU
+Optimizing NNI: done in 0.000846299 secs using 99.96% CPU
+Optimizing NNI: done in 0.00109782 secs using 99.93% CPU
+Optimizing NNI: done in 0.000360283 secs using 99.64% CPU
+Optimizing NNI: done in 0.000345605 secs using 99.82% CPU
+Optimizing NNI: done in 0.0003536 secs using 99.83% CPU
+Optimizing NNI: done in 0.0008306 secs using 99.81% CPU
+Optimizing NNI: done in 0.0010938 secs
+Optimizing NNI: done in 0.000295702 secs using 14.54% CPU
+Iteration 80 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.0009166 secs using 99.93% CPU
+Optimizing NNI: done in 0.00034821 secs using 99.94% CPU
+Optimizing NNI: done in 0.000359991 secs using 99.72% CPU
+Optimizing NNI: done in 0.00035398 secs using 99.72% CPU
+Optimizing NNI: done in 0.000372205 secs using 99.68% CPU
+Optimizing NNI: done in 0.00147208 secs using 99.93% CPU
+Optimizing NNI: done in 0.000850837 secs
+Optimizing NNI: done in 0.00072314 secs using 99.84% CPU
+Optimizing NNI: done in 0.000748617 secs using 99.92% CPU
+Optimizing NNI: done in 0.000806736 secs
+Iteration 90 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000876476 secs using 99.83% CPU
+Optimizing NNI: done in 0.000908435 secs using 91.81% CPU
+Optimizing NNI: done in 0.000869823 secs
+Optimizing NNI: done in 0.00122169 secs using 99.94% CPU
+Optimizing NNI: done in 0.000743176 secs using 98.5% CPU
+Optimizing NNI: done in 0.000725324 secs using 99.96% CPU
+Optimizing NNI: done in 0.00125769 secs using 71.48% CPU
+Optimizing NNI: done in 0.000752264 secs
+Optimizing NNI: done in 0.000865786 secs using 40.08% CPU
+Optimizing NNI: done in 0.000896964 secs using 94.65% CPU
+Iteration 100 / LogL: -667.321 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000809481 secs using 99.82% CPU
+Optimizing NNI: done in 0.000762362 secs using 99.95% CPU
+Optimizing NNI: done in 0.00033809 secs using 99.68% CPU
+Optimizing NNI: done in 0.000764076 secs using 99.86% CPU
+Optimizing NNI: done in 0.000792168 secs using 99.85% CPU
+Optimizing NNI: done in 0.000916651 secs using 99.93% CPU
+Optimizing NNI: done in 0.000726776 secs using 97.55% CPU
+Optimizing NNI: done in 0.000840889 secs using 99.89% CPU
+Optimizing NNI: done in 0.000774024 secs using 100% CPU
+Optimizing NNI: done in 0.000797398 secs using 99.82% CPU
+Iteration 110 / LogL: -681.818 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000748807 secs using 99.89% CPU
+Optimizing NNI: done in 0.00158208 secs using 99.93% CPU
+Optimizing NNI: done in 0.000308415 secs
+Optimizing NNI: done in 0.000764627 secs using 40.67% CPU
+Optimizing NNI: done in 0.000926338 secs using 94.89% CPU
+Optimizing NNI: done in 0.000768093 secs using 99.86% CPU
+Optimizing NNI: done in 0.000772903 secs using 99.88% CPU
+Optimizing NNI: done in 0.00116591 secs using 99.92% CPU
+Optimizing NNI: done in 0.00122699 secs using 100% CPU
+Optimizing NNI: done in 0.000839707 secs using 99.92% CPU
+Iteration 120 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000833786 secs using 99.91% CPU
+Optimizing NNI: done in 0.000903987 secs using 100% CPU
+Optimizing NNI: done in 0.000847632 secs using 99.93% CPU
+Optimizing NNI: done in 0.000742114 secs
+Optimizing NNI: done in 0.000843443 secs using 89.4% CPU
+Optimizing NNI: done in 0.00151669 secs using 99.95% CPU
+Optimizing NNI: done in 0.000345975 secs using 99.43% CPU
+Optimizing NNI: done in 0.00160859 secs using 54.52% CPU
+Optimizing NNI: done in 0.00124916 secs using 92.38% CPU
+Optimizing NNI: done in 0.00128647 secs using 99.89% CPU
+Iteration 130 / LogL: -667.321 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.00112329 secs using 97.3% CPU
+Optimizing NNI: done in 0.000811845 secs using 99.9% CPU
+Optimizing NNI: done in 0.000808618 secs using 99.8% CPU
+Optimizing NNI: done in 0.000902333 secs
+Optimizing NNI: done in 0.000832444 secs using 99.95% CPU
+Optimizing NNI: done in 0.00160412 secs using 99.99% CPU
+Optimizing NNI: done in 0.000343622 secs using 97.78% CPU
+Optimizing NNI: done in 0.000795494 secs using 99.94% CPU
+Optimizing NNI: done in 0.00127957 secs using 99.8% CPU
+Optimizing NNI: done in 0.000779094 secs using 99.86% CPU
+Iteration 140 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
+Optimizing NNI: done in 0.000791758 secs using 99.78% CPU
+Optimizing NNI: done in 0.000711467 secs using 99.93% CPU
+Optimizing NNI: done in 0.00133779 secs
+Optimizing NNI: done in 0.000297655 secs using 90.37% CPU
+Optimizing NNI: done in 0.00164192 secs using 99.94% CPU
+Optimizing NNI: done in 0.00125657 secs using 99.88% CPU
+Optimizing NNI: done in 0.000362577 secs using 99.84% CPU
+Optimizing NNI: done in 0.000813007 secs using 99.88% CPU
+Optimizing NNI: done in 0.00104986 secs using 99.92% CPU
+TREE SEARCH COMPLETED AFTER 149 ITERATIONS / Time: 0h:0m:0s
+
+--------------------------------------------------------------------
+|                    FINALIZING TREE SEARCH                        |
+--------------------------------------------------------------------
+Performs final model parameters optimization
+Estimate model parameters (epsilon = 0.010)
+1. Initial log-likelihood: -667.319
+Optimal log-likelihood: -667.319
+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 : -667.319
+Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.state
+Total tree length: 0.082
+
+Total number of iterations: 149
+CPU time used for tree search: 0.181 sec (0h:0m:0s)
+Wall-clock time used for tree search: 0.195 sec (0h:0m:0s)
+Total CPU time used: 0.318 sec (0h:0m:0s)
+Total wall-clock time used: 0.344 sec (0h:0m:0s)
+
+Analysis results written to: 
+  IQ-TREE report:                /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree
+  Maximum-likelihood tree:       /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile
+  Likelihood distances:          /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist
+  Ancestral state:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.state
+  Screen log file:               /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/out.log
+
+Date and Time: Mon Aug 18 15:31:53 2025

test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist

@@ -0,0 +1,13 @@
+12
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