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

test/ref-results/partition-new-simu/iqtree/iclust-0/log

@@ -6,22 +6,22 @@ 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:    580837 (Using SPRNG - Scalable Parallel Random Number Generator)
-Time:    Sat Aug 16 23:08:16 2025
+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 0.000107562 secs using 59.5% CPU
+Reading fasta file: done in 0.000109043 secs using 65.11% CPU
 Alignment most likely contains DNA/RNA sequences
-Constructing alignment: done in 0.000288013 secs using 60.07% CPU
+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 5.541e-06 secs using 54.14% CPU
+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%
@@ -41,16 +41,16 @@ Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000
 Perform fast likelihood tree search using GTR+I+G model...
 Estimate model parameters (epsilon = 5.000)
 Perform nearest neighbor interchange...
-Optimizing NNI: done in 0.000604378 secs
+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: 0.93501  A-G: 0.93474  A-T: 0.45114  C-G: 0.67930  C-T: 0.80175  G-T: 1.00000
+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: 0.004 seconds
+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) ...
@@ -58,7 +58,7 @@ ModelFinder will test up to 968 DNA models (sample size: 352 epsilon: 0.100) ...
   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     1385.754     1471.251
+  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
@@ -102,7 +102,7 @@ ModelFinder will test up to 968 DNA models (sample size: 352 epsilon: 0.100) ...
 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     1383.042     1468.539
+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
@@ -133,12 +133,12 @@ ModelFinder will test up to 968 DNA models (sample size: 352 epsilon: 0.100) ...
 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  1383.481     1387.468     1480.071
+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  1383.481     1387.468     1480.071
+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  1381.481     1385.150     1474.208
+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
@@ -189,7 +189,7 @@ ModelFinder will test up to 968 DNA models (sample size: 352 epsilon: 0.100) ...
 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     1389.063     1495.704
+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
@@ -198,7 +198,7 @@ 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: 0.120 seconds (0h:0m:0s)
+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!
@@ -210,11 +210,11 @@ 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 0.000415974 secs using 95.44% CPU
-Computing ML distances took 0.000445 sec (of wall-clock time) 0.000430 sec (of CPU time)
-Setting up auxiliary I and S matrices: done in 3.6279e-05 secs using 96.47% CPU
-Constructing RapidNJ tree: done in 5.6416e-05 secs using 97.49% CPU
-Computing RapidNJ tree took 0.000115 sec (of wall-clock time) 0.000115 sec (of CPU time)
+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                      |
@@ -224,33 +224,29 @@ 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 0.000608887 secs using 94.27% CPU
+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 0.000595683 secs using 98.37% CPU
-Optimizing NNI: done in 0.000607454 secs
-BETTER TREE FOUND at iteration 3: -667.319
-Optimizing NNI: done in 0.000607845 secs using 65.64% CPU
-BETTER TREE FOUND at iteration 4: -667.319
-Optimizing NNI: done in 0.000580934 secs using 99.67% CPU
-Optimizing NNI: done in 0.000583148 secs using 96.54% CPU
-Optimizing NNI: done in 0.000633383 secs
-Optimizing NNI: done in 0.000584451 secs using 67.93% CPU
-Optimizing NNI: done in 0.000567198 secs using 93.27% CPU
-Optimizing NNI: done in 0.000575274 secs using 99.78% CPU
+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 0.00060517 secs using 99.81% CPU
-Optimizing NNI: done in 0.000586796 secs using 99.86% CPU
-Optimizing NNI: done in 0.000563982 secs using 99.83% CPU
-BETTER TREE FOUND at iteration 13: -667.319
-Optimizing NNI: done in 0.000541149 secs using 99.79% CPU
-BETTER TREE FOUND at iteration 14: -667.319
-Optimizing NNI: done in 0.000550627 secs
-Optimizing NNI: done in 0.000536621 secs using 41% CPU
-Optimizing NNI: done in 0.000570264 secs using 99.78% CPU
-Optimizing NNI: done in 0.000611872 secs using 99.69% CPU
-Optimizing NNI: done in 0.000581445 secs using 97% CPU
-Optimizing NNI: done in 0.000601262 secs using 99.79% CPU
+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
@@ -258,111 +254,151 @@ Number of iterations: 20
 --------------------------------------------------------------------
 |               OPTIMIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Optimizing NNI: done in 0.00134074 secs using 99.35% CPU
-Optimizing NNI: done in 0.000758749 secs using 99.11% CPU
-Optimizing NNI: done in 0.000368644 secs using 99.28% CPU
-Optimizing NNI: done in 0.00118484 secs using 99.93% CPU
-Optimizing NNI: done in 0.000346834 secs using 99.76% CPU
-Optimizing NNI: done in 0.00117798 secs using 99.92% CPU
-Optimizing NNI: done in 0.000798614 secs using 99.67% CPU
-Optimizing NNI: done in 0.00035576 secs using 99.79% CPU
-Optimizing NNI: done in 0.000346773 secs using 99.78% CPU
-Optimizing NNI: done in 0.000790299 secs using 99.84% CPU
+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 0.000343177 secs using 99.66% CPU
-Optimizing NNI: done in 0.000714375 secs using 99.81% CPU
-Optimizing NNI: done in 0.00106988 secs using 99.92% CPU
-Optimizing NNI: done in 0.000829973 secs using 99.88% CPU
-Optimizing NNI: done in 0.000333128 secs using 99.66% CPU
-Optimizing NNI: done in 0.000788896 secs
-Optimizing NNI: done in 0.000364797 secs using 84.16% CPU
-Optimizing NNI: done in 0.00119208 secs using 99.83% CPU
-Optimizing NNI: done in 0.00075415 secs using 99.85% CPU
-Optimizing NNI: done in 0.000856874 secs
-Iteration 40 / LogL: -667.321 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000758088 secs using 43.66% CPU
-Optimizing NNI: done in 0.000691823 secs using 96.41% CPU
-Optimizing NNI: done in 0.000343397 secs using 99.59% CPU
-Optimizing NNI: done in 0.00147757 secs using 99.96% CPU
-Optimizing NNI: done in 0.00105325 secs using 99.88% CPU
-Optimizing NNI: done in 0.000789788 secs using 99.9% CPU
-Optimizing NNI: done in 0.000745214 secs using 99.84% CPU
-Optimizing NNI: done in 0.000802211 secs using 99.85% CPU
-Optimizing NNI: done in 0.000730427 secs using 99.94% CPU
-Optimizing NNI: done in 0.000763078 secs using 99.99% CPU
-Iteration 50 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.00090765 secs using 99.82% CPU
-Optimizing NNI: done in 0.000344679 secs using 99.8% CPU
-Optimizing NNI: done in 0.000882542 secs using 99.94% CPU
-Optimizing NNI: done in 0.0016301 secs using 38.71% CPU
-Optimizing NNI: done in 0.000741506 secs using 99.93% CPU
-Optimizing NNI: done in 0.00078036 secs using 99.83% CPU
-Optimizing NNI: done in 0.00090244 secs using 99.84% CPU
-Optimizing NNI: done in 0.000764611 secs using 99.79% CPU
-Optimizing NNI: done in 0.000351702 secs using 99.8% CPU
-Optimizing NNI: done in 0.000375086 secs using 99.71% CPU
-Iteration 60 / LogL: -667.319 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.00070603 secs using 99.85% CPU
-Optimizing NNI: done in 0.000756785 secs using 99.9% CPU
-Optimizing NNI: done in 0.0007115 secs using 99.93% CPU
-Optimizing NNI: done in 0.000730345 secs using 99.82% CPU
-Optimizing NNI: done in 0.000788084 secs using 99.99% CPU
-Optimizing NNI: done in 0.000845403 secs using 99.83% CPU
-Optimizing NNI: done in 0.000362984 secs using 99.73% CPU
-Optimizing NNI: done in 0.00156261 secs using 99.9% CPU
-Optimizing NNI: done in 0.000876562 secs
-Optimizing NNI: done in 0.000346553 secs using 92.63% CPU
+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 0.000326074 secs using 92.92% CPU
-Optimizing NNI: done in 0.00118572 secs using 99.77% CPU
-Optimizing NNI: done in 0.00080144 secs
-Optimizing NNI: done in 0.000655575 secs using 14.34% CPU
-Optimizing NNI: done in 0.000726329 secs using 99.95% CPU
-Optimizing NNI: done in 0.000344188 secs
-Optimizing NNI: done in 0.000760743 secs using 43.12% CPU
-Optimizing NNI: done in 0.00153436 secs using 97.3% CPU
-Optimizing NNI: done in 0.00033425 secs using 99.63% CPU
-Optimizing NNI: done in 0.000330071 secs using 99.68% CPU
+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 0.000486075 secs using 99.78% CPU
-Optimizing NNI: done in 0.000779359 secs using 99.83% CPU
-Optimizing NNI: done in 0.00106454 secs using 99.86% CPU
-Optimizing NNI: done in 0.000331564 secs using 99.53% CPU
-Optimizing NNI: done in 0.000873555 secs using 99.82% CPU
-Optimizing NNI: done in 0.000833079 secs using 99.87% CPU
-Optimizing NNI: done in 0.000726369 secs using 99.81% CPU
-Optimizing NNI: done in 0.00141428 secs using 99.91% CPU
-Optimizing NNI: done in 0.000380376 secs using 99.64% CPU
-Optimizing NNI: done in 0.000736337 secs using 98.73% CPU
+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 0.000653691 secs using 99.89% CPU
-Optimizing NNI: done in 0.000725557 secs using 99.79% CPU
-Optimizing NNI: done in 0.000874427 secs using 99.84% CPU
-Optimizing NNI: done in 0.000835223 secs using 99.97% CPU
-Optimizing NNI: done in 0.000680301 secs using 99.96% CPU
-Optimizing NNI: done in 0.000755083 secs using 99.86% CPU
-Optimizing NNI: done in 0.001132 secs using 11.84% CPU
-Optimizing NNI: done in 0.000330262 secs using 99.62% CPU
-Optimizing NNI: done in 0.000321756 secs using 99.45% CPU
-Optimizing NNI: done in 0.000781652 secs using 99.79% CPU
-Iteration 100 / LogL: -667.320 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.00089204 secs using 99.88% CPU
-Optimizing NNI: done in 0.00118078 secs using 69.11% CPU
-Optimizing NNI: done in 0.000814935 secs using 44.79% CPU
-Optimizing NNI: done in 0.000769389 secs using 97.35% CPU
-Optimizing NNI: done in 0.00108522 secs using 99.89% CPU
-Optimizing NNI: done in 0.000333828 secs using 98.85% CPU
-Optimizing NNI: done in 0.000667467 secs
-Optimizing NNI: done in 0.000810907 secs
-Optimizing NNI: done in 0.00150203 secs using 85.08% CPU
-Optimizing NNI: done in 0.000785881 secs using 99.89% CPU
-Iteration 110 / LogL: -677.602 / Time: 0h:0m:0s (0h:0m:0s left)
-Optimizing NNI: done in 0.000341403 secs using 99.59% CPU
-Optimizing NNI: done in 0.000831426 secs using 99.83% CPU
-Optimizing NNI: done in 0.000757998 secs using 99.87% CPU
-Optimizing NNI: done in 0.00115071 secs using 13.64% CPU
-Optimizing NNI: done in 0.000726449 secs using 99.8% CPU
-TREE SEARCH COMPLETED AFTER 115 ITERATIONS / Time: 0h:0m:0s
+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                        |
@@ -378,11 +414,11 @@ 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: 115
-CPU time used for tree search: 0.140 sec (0h:0m:0s)
-Wall-clock time used for tree search: 0.147 sec (0h:0m:0s)
-Total CPU time used: 0.274 sec (0h:0m:0s)
-Total wall-clock time used: 0.296 sec (0h:0m:0s)
+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
@@ -391,4 +427,4 @@ Analysis results written to:
   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: Sat Aug 16 23:08:16 2025
+Date and Time: Mon Aug 18 15:31:53 2025

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

@@ -2,7 +2,7 @@ IQ-TREE 3.0.1 built May  5 2025
 
 Input file name: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa
 Type of analysis: ModelFinder + tree reconstruction
-Random seed number: 580837
+Random seed number: 769287
 
 REFERENCES
 ----------
@@ -54,7 +54,7 @@ JC+G4              -667.320    1378.641 -   0.0174    1381.717 -    0.022    146
 JC+G4              -667.320    1378.641 -   0.0174    1381.717 -    0.022    1463.640 -   0.0149
 F81+G4             -667.320    1378.641 -   0.0174    1381.717 -    0.022    1463.641 -   0.0149
 F81+F              -663.546    1375.093 +    0.103    1378.763 +   0.0964    1467.820 -  0.00185
-K3Pu               -666.838    1379.676 -   0.0104    1383.042 -   0.0114    1468.539 -  0.00129
+K3Pu               -666.838    1379.676 -   0.0104    1383.041 -   0.0114    1468.539 -  0.00129
 K3P                -666.838    1379.676 -   0.0104    1383.042 -   0.0113    1468.539 -  0.00129
 K3P                -666.838    1379.676 -   0.0104    1383.042 -   0.0113    1468.539 -  0.00129
 TPM2u              -667.114    1380.228 -  0.00788    1383.594 -  0.00861    1469.092 - 0.000978
@@ -72,12 +72,12 @@ K2P+I              -667.283    1380.566 -  0.00665    1383.932 -  0.00727    146
 HKY+G4             -667.284    1380.568 -  0.00665    1383.934 -  0.00727    1469.431 - 0.000826
 K2P+G4             -667.284    1380.568 -  0.00665    1383.934 -  0.00727    1469.431 - 0.000826
 K2P+G4             -667.284    1380.568 -  0.00665    1383.934 -  0.00727    1469.431 - 0.000826
-JC+R2              -667.320    1380.640 -  0.00641    1384.006 -  0.00701    1469.503 - 0.000797
-JC+I+G4            -668.194    1382.388 -  0.00268    1385.754 -  0.00292    1471.251 - 0.000332
+JC+R2              -667.320    1380.640 -  0.00641    1384.006 -  0.00701    1469.503 - 0.000796
+JC+I+G4            -668.194    1382.388 -  0.00268    1385.753 -  0.00292    1471.251 - 0.000332
 HKY+F              -663.502    1377.004 -   0.0395    1380.992 -   0.0316    1473.595 - 0.000103
 F81+F+I            -663.546    1377.093 -   0.0378    1381.081 -   0.0303    1473.684 - 9.85e-05
 F81+F+G4           -663.547    1377.095 -   0.0377    1381.082 -   0.0302    1473.685 - 9.84e-05
-TIM                -666.740    1381.481 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
+TIM                -666.740    1381.480 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
 TIMe               -666.740    1381.481 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
 TIMe               -666.740    1381.481 -  0.00421    1385.150 -  0.00395    1474.208 - 7.58e-05
 K3Pu+I             -666.838    1381.676 -  0.00382    1385.345 -  0.00359    1474.403 - 6.88e-05
@@ -121,17 +121,17 @@ TVM                -666.493    1382.987 -  0.00198    1386.975 -  0.00159    147
 TVMe               -666.493    1382.987 -  0.00198    1386.975 -  0.00159    1479.578 - 5.17e-06
 TVMe               -666.493    1382.987 -  0.00198    1386.975 -  0.00159    1479.578 - 5.17e-06
 TIM+I              -666.740    1383.480 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
-TIMe+I             -666.740    1383.481 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
-TIMe+I             -666.740    1383.481 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
+TIMe+I             -666.740    1383.480 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
+TIMe+I             -666.740    1383.480 -  0.00155    1387.468 -  0.00124    1480.071 - 4.04e-06
 TIM+G4             -666.741    1383.482 -  0.00155    1387.470 -  0.00124    1480.073 - 4.04e-06
 TIMe+G4            -666.741    1383.482 -  0.00155    1387.470 -  0.00124    1480.073 - 4.04e-06
 TIMe+G4            -666.741    1383.482 -  0.00155    1387.470 -  0.00124    1480.073 - 4.04e-06
 TIM2e+I            -667.017    1384.033 -  0.00118    1388.021 - 0.000941    1480.624 - 3.06e-06
 TIM2+I             -667.017    1384.033 -  0.00118    1388.021 - 0.000941    1480.624 - 3.06e-06
 TIM2e+I            -667.017    1384.033 -  0.00118    1388.021 - 0.000941    1480.624 - 3.06e-06
-TIM2e+G4           -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
 TIM2+G4            -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
 TIM2e+G4           -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
+TIM2e+G4           -667.017    1384.035 -  0.00117    1388.023 - 0.000941    1480.626 - 3.06e-06
 TIM3+I             -667.143    1384.287 -  0.00104    1388.275 - 0.000829    1480.878 -  2.7e-06
 TIM3e+I            -667.144    1384.287 -  0.00104    1388.275 - 0.000829    1480.878 -  2.7e-06
 TIM3e+I            -667.144    1384.287 -  0.00104    1388.275 - 0.000829    1480.878 -  2.7e-06
@@ -173,7 +173,7 @@ SYM+I              -666.396    1386.793 - 0.000296    1391.459 - 0.000169    149
 GTR+G4             -666.397    1386.794 - 0.000296    1391.461 - 0.000169    1491.112 - 1.62e-08
 SYM+G4             -666.397    1386.794 - 0.000296    1391.461 - 0.000169    1491.113 - 1.62e-08
 SYM+G4             -666.397    1386.794 - 0.000296    1391.461 - 0.000169    1491.113 - 1.62e-08
-GTR+F              -662.829    1383.659 -  0.00142    1389.063 - 0.000559    1495.704 - 1.63e-09
+GTR+F              -662.829    1383.659 -  0.00142    1389.062 - 0.000559    1495.704 - 1.63e-09
 TVM+F+I            -662.870    1383.740 -  0.00136    1389.144 - 0.000537    1495.786 - 1.56e-09
 TVM+F+G4           -662.871    1383.742 -  0.00136    1389.146 - 0.000536    1495.787 - 1.56e-09
 GTR+F+I            -662.829    1385.659 - 0.000521    1391.453 - 0.000169    1501.568 - 8.68e-11
@@ -222,7 +222,7 @@ Corrected Akaike information criterion (AICc) score: 1379.4388
 Bayesian information criterion (BIC) score: 1457.7751
 
 Total tree length (sum of branch lengths): 0.0816
-Sum of internal branch lengths: 0.0175 (21.4391% of tree length)
+Sum of internal branch lengths: 0.0175 (21.4403% of tree length)
 
 WARNING: 6 near-zero internal branches (<0.0028) should be treated with caution
          Such branches are denoted by '**' in the figure below
@@ -231,31 +231,31 @@ NOTE: Tree is UNROOTED although outgroup taxon 'XnaiveX' is drawn at root
 
 +**XnaiveX
 | (Node1)
-|                      +------------------------------------18f4019708
-|                   +**| (Node5)
-|                   |  |                             +-------------ee25049b92
-|                   |  +-----------------------------| (Node6)
-|                   |                                +------9c3cedb840
-|                +**| (Node4)
-|                |  |             +**648902c3e5
-|                |  +-------------| (Node7)
-|                |                |  +**8024ed1a22
-|                |                +**| (Node8)
-|                |                   +**f47122f1f5
-|             +**| (Node3)
-|             |  |  +----------------------------308de1d739
-|             |  +**| (Node9)
-|             |     +---------------------efdea248af
-+-------------| (Node2)
-|             +------------------------------------5fb484a8a6
+|                +------------------------------------18f4019708
+|  +-------------| (Node3)
+|  |             |     +----------------------------308de1d739
+|  |             |  +**| (Node5)
+|  |             |  |  +---------------------efdea248af
+|  |             +**| (Node4)
+|  |                |     +------------------------------------5fb484a8a6
+|  |                |  +**| (Node7)
+|  |                |  |  |                             +-------------ee25049b92
+|  |                |  |  +-----------------------------| (Node8)
+|  |                |  |                                +------9c3cedb840
+|  |                +**| (Node6)
+|  |                   |             +**648902c3e5
+|  |                   +-------------| (Node9)
+|  |                                 |  +**8024ed1a22
+|  |                                 +**| (Node10)
+|  |                                    +**f47122f1f5
++**| (Node2)
+|  +**d024e5cab0
 |
-|  +**822801f8ab
-+**| (Node10)
-   +**d024e5cab0
++**822801f8ab
 
 Tree in newick format:
 
-(XnaiveX:0.0000010000,((((18f4019708:0.0145918997,(ee25049b92:0.0058202340,9c3cedb840:0.0028896479)Node6:0.0116795079)Node5:0.0000010000,(648902c3e5:0.0000010000,(8024ed1a22:0.0000010000,f47122f1f5:0.0000010000)Node8:0.0000010000)Node7:0.0058027364)Node4:0.0000010000,(308de1d739:0.0116507187,efdea248af:0.0087210277)Node9:0.0000010000)Node3:0.0000010000,5fb484a8a6:0.0145919018)Node2:0.0058027334,(822801f8ab:0.0000010000,d024e5cab0:0.0000010000)Node10:0.0000010000)Node1;
+(XnaiveX:0.0000010000,((18f4019708:0.0145918999,((308de1d739:0.0116507178,efdea248af:0.0087210277)Node5:0.0000010000,((5fb484a8a6:0.0145918997,(ee25049b92:0.0058202340,9c3cedb840:0.0028896479)Node8:0.0116795079)Node7:0.0000010000,(648902c3e5:0.0000010000,(8024ed1a22:0.0000010000,f47122f1f5:0.0000010000)Node10:0.0000010000)Node9:0.0058027364)Node6:0.0000010000)Node4:0.0000010000)Node3:0.0058027364,d024e5cab0:0.0000010000)Node2:0.0000010000,822801f8ab:0.0000010000)Node1;
 
 ALISIM COMMAND
 --------------
@@ -276,7 +276,7 @@ For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim
 TIME STAMP
 ----------
 
-Date and time: Sat Aug 16 23:08:16 2025
-Total CPU time used: 0.273774 seconds (0h:0m:0s)
-Total wall-clock time used: 0.29702 seconds (0h:0m:0s)
+Date and time: Mon Aug 18 15:31:53 2025
+Total CPU time used: 0.317828 seconds (0h:0m:0s)
+Total wall-clock time used: 0.34555 seconds (0h:0m:0s)