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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (95) hide show
  1. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +95 -95
  3. test/new-results/get-selection-metrics-new-simu.yaml +1 -1
  4. test/new-results/test.log +2 -2
  5. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  8. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
  9. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  25. test/paired/new-results/run-times.csv +6 -6
  26. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -6
  27. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
  28. test/paired/new-results/subset-partition-new-simu/merged-partition.log +3 -3
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  32. test/paired/new-results/test.log +33 -33
  33. test/ref-results/partition-new-simu/iqtree/iclust-0/log +187 -151
  34. test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
  35. test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +34 -34
  36. test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +187 -151
  37. test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
  38. test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +2820 -2820
  39. test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -1
  40. test/ref-results/partition-new-simu/iqtree/iclust-1/log +166 -207
  41. test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
  42. test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +151 -151
  43. test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +166 -207
  44. test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
  45. test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +740 -740
  46. test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -1
  47. test/ref-results/partition-new-simu/iqtree/iclust-2/log +134 -135
  48. test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
  49. test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +17 -17
  50. test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +134 -135
  51. test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
  52. test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +763 -763
  53. test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -1
  54. test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -1
  55. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +30 -30
  56. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +7 -7
  57. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -1
  58. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -1
  59. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -1
  60. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  61. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +87 -87
  62. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -20
  63. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -20
  64. test/ref-results/partition-new-simu/raxml/iclust-0/log +198 -197
  65. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -1
  66. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -1
  67. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  68. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +54 -54
  69. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -20
  70. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -20
  71. test/ref-results/partition-new-simu/raxml/iclust-1/log +112 -112
  72. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +22 -22
  73. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -6
  74. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -1
  75. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -1
  76. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -1
  77. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  78. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +84 -84
  79. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -20
  80. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -20
  81. test/ref-results/partition-new-simu/raxml/iclust-2/log +182 -182
  82. test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -1
  83. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  84. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  85. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  86. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  87. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
  88. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  89. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
  90. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
  91. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
  92. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
  93. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
  94. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
  95. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
test/ref-results/partition-new-simu/iqtree/iclust-1/out.log CHANGED
@@ -5,22 +5,22 @@ Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt
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  Host: pkrvmubgrv54qmi (AVX2, FMA3, 15 GB RAM)
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  Command: /home/runner/work/partis/partis/bin/iqtree3_intel -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out -o XnaiveX
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- Seed: 596149 (Using SPRNG - Scalable Parallel Random Number Generator)
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- Time: Sat Aug 16 23:08:16 2025
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+ Seed: 784887 (Using SPRNG - Scalable Parallel Random Number Generator)
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+ Time: Mon Aug 18 15:31:52 2025
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  Kernel: AVX+FMA - 1 threads (4 CPU cores detected)
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  HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
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  HINT: -nt AUTO will automatically determine the best number of threads to use.
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  Reading alignment file /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa ... Fasta format detected
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- Reading fasta file: done in 7.981e-05 secs using 48.87% CPU
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+ Reading fasta file: done in 7.5741e-05 secs
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  Alignment most likely contains DNA/RNA sequences
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- Constructing alignment: done in 0.000370789 secs using 19.69% CPU
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+ Constructing alignment: done in 0.000379799 secs
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  WARNING: 3 sites contain only gaps or ambiguous characters.
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  Alignment has 8 sequences with 370 columns, 7 distinct patterns
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  0 parsimony-informative, 2 singleton sites, 368 constant sites
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  Gap/Ambiguity Composition p-value
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- Analyzing sequences: done in 7.454e-06 secs
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+ Analyzing sequences: done in 6.192e-06 secs
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  1 XnaiveX 0.81% passed 100.00%
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  2 13de8675ec 0.81% passed 100.00%
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  3 20a0129b57 0.81% passed 99.96%
@@ -36,17 +36,17 @@ Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000
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  Perform fast likelihood tree search using GTR+I+G model...
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  Estimate model parameters (epsilon = 5.000)
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  Perform nearest neighbor interchange...
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- Optimizing NNI: done in 0.000214284 secs using 98.93% CPU
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+ Optimizing NNI: done in 0.000308676 secs using 59.61% CPU
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  Estimate model parameters (epsilon = 1.000)
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  1. Initial log-likelihood: -519.628
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  Optimal log-likelihood: -519.601
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- Rate parameters: A-C: 0.00010 A-G: 3.78714 A-T: 0.00010 C-G: 0.00010 C-T: 0.00010 G-T: 1.00000
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+ Rate parameters: A-C: 0.00010 A-G: 3.78712 A-T: 0.00010 C-G: 0.00010 C-T: 0.00010 G-T: 1.00000
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  Warning! Some parameters hit the boundaries
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  Base frequencies: A: 0.237 C: 0.270 G: 0.294 T: 0.199
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  Proportion of invariable sites: 0.497
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  Gamma shape alpha: 998.448
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  Parameters optimization took 1 rounds (0.001 sec)
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- Time for fast ML tree search: 0.002 seconds
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+ Time for fast ML tree search: 0.003 seconds
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  NOTE: ModelFinder requires 0 MB RAM!
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  ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
@@ -89,15 +89,15 @@ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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  221 TN 524.028 15 1078.055 1079.411 1136.758
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  222 TN+I 524.028 16 1080.055 1081.596 1142.671
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  223 TN+G4 524.028 16 1080.055 1081.596 1142.671
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- 243 TN+F 520.525 18 1077.050 1078.999 1147.494
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- 244 TN+F+I 520.525 19 1079.050 1081.222 1153.407
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+ 243 TN+F 520.525 18 1077.050 1078.999 1147.493
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+ 244 TN+F+I 520.525 19 1079.051 1081.222 1153.407
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  245 TN+F+G4 520.525 19 1079.050 1081.222 1153.407
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- 265 K3P 523.994 15 1077.988 1079.344 1136.690
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- 266 K3P+I 523.998 16 1079.996 1081.537 1142.612
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- 267 K3P+G4 523.996 16 1079.992 1081.533 1142.608
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- 287 K3P 523.994 15 1077.988 1079.344 1136.690
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- 288 K3P+I 523.998 16 1079.996 1081.537 1142.612
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- 289 K3P+G4 523.996 16 1079.992 1081.533 1142.608
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+ 265 K3P 523.995 15 1077.990 1079.346 1136.693
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+ 266 K3P+I 523.988 16 1079.976 1081.517 1142.592
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+ 267 K3P+G4 523.996 16 1079.991 1081.532 1142.607
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+ 287 K3P 523.995 15 1077.990 1079.346 1136.693
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+ 288 K3P+I 523.988 16 1079.976 1081.517 1142.592
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+ 289 K3P+G4 523.996 16 1079.991 1081.532 1142.607
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  309 K3Pu 523.971 15 1077.941 1079.297 1136.644
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  310 K3Pu+I 523.970 16 1079.940 1081.481 1142.556
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  311 K3Pu+G4 523.970 16 1079.940 1081.481 1142.556
@@ -106,10 +106,10 @@ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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  333 K3Pu+F+G4 520.390 19 1078.780 1080.952 1153.137
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  353 TPM2 524.023 15 1078.046 1079.402 1136.749
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  354 TPM2+I 524.023 16 1080.046 1081.587 1142.662
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- 355 TPM2+G4 524.023 16 1080.046 1081.587 1142.662
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+ 355 TPM2+G4 524.023 16 1080.046 1081.588 1142.663
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  375 TPM2 524.023 15 1078.046 1079.402 1136.749
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  376 TPM2+I 524.023 16 1080.046 1081.587 1142.662
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- 377 TPM2+G4 524.023 16 1080.046 1081.587 1142.662
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+ 377 TPM2+G4 524.023 16 1080.046 1081.588 1142.663
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  397 TPM2u 524.023 15 1078.046 1079.402 1136.749
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  398 TPM2u+I 524.023 16 1080.046 1081.587 1142.662
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  399 TPM2u+G4 524.023 16 1080.046 1081.587 1142.662
@@ -125,30 +125,30 @@ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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  485 TPM3u 523.895 15 1077.791 1079.147 1136.493
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  486 TPM3u+I 523.895 16 1079.791 1081.332 1142.407
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  487 TPM3u+G4 523.895 16 1079.791 1081.332 1142.407
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- 507 TPM3u+F 520.242 18 1076.484 1078.433 1146.927
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+ 507 TPM3u+F 520.242 18 1076.484 1078.433 1146.928
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  508 TPM3u+F+I 520.242 19 1078.484 1080.656 1152.841
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  509 TPM3u+F+G4 520.242 19 1078.484 1080.656 1152.841
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- 529 TIMe 523.740 16 1079.479 1081.021 1142.096
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- 530 TIMe+I 523.733 17 1081.466 1083.205 1147.996
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- 531 TIMe+G4 523.726 17 1081.452 1083.191 1147.982
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- 551 TIMe 523.740 16 1079.479 1081.021 1142.096
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- 552 TIMe+I 523.733 17 1081.466 1083.205 1147.996
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- 553 TIMe+G4 523.726 17 1081.452 1083.191 1147.982
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- 573 TIM 523.733 16 1079.466 1081.007 1142.082
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- 574 TIM+I 523.726 17 1081.452 1083.191 1147.982
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- 575 TIM+G4 523.719 17 1081.439 1083.177 1147.968
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- 595 TIM+F 519.817 19 1077.635 1079.806 1151.991
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- 596 TIM+F+I 519.818 20 1079.635 1082.042 1157.905
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- 597 TIM+F+G4 519.817 20 1079.635 1082.042 1157.905
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- 617 TIM2e 523.390 16 1078.779 1080.320 1141.395
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- 618 TIM2e+I 523.390 17 1080.779 1082.518 1147.309
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- 619 TIM2e+G4 523.390 17 1080.779 1082.518 1147.309
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- 639 TIM2e 523.390 16 1078.779 1080.320 1141.395
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- 640 TIM2e+I 523.390 17 1080.779 1082.518 1147.309
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- 641 TIM2e+G4 523.390 17 1080.779 1082.518 1147.309
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- 661 TIM2 523.390 16 1078.779 1080.320 1141.395
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- 662 TIM2+I 523.390 17 1080.779 1082.518 1147.309
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- 663 TIM2+G4 523.390 17 1080.779 1082.518 1147.309
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+ 529 TIMe 523.336 16 1078.671 1080.213 1141.288
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+ 530 TIMe+I 523.336 17 1080.671 1082.410 1147.201
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+ 531 TIMe+G4 523.336 17 1080.672 1082.410 1147.201
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+ 551 TIMe 523.336 16 1078.671 1080.213 1141.288
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+ 552 TIMe+I 523.336 17 1080.671 1082.410 1147.201
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+ 553 TIMe+G4 523.336 17 1080.672 1082.410 1147.201
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+ 573 TIM 523.336 16 1078.671 1080.213 1141.288
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+ 574 TIM+I 523.336 17 1080.671 1082.410 1147.201
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+ 575 TIM+G4 523.336 17 1080.672 1082.410 1147.201
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+ 595 TIM+F 519.818 19 1077.635 1079.806 1151.992
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+ 596 TIM+F+I 519.818 20 1079.636 1082.042 1157.906
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+ 597 TIM+F+G4 519.818 20 1079.635 1082.042 1157.905
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+ 617 TIM2e 523.390 16 1078.780 1080.321 1141.396
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+ 618 TIM2e+I 523.390 17 1080.780 1082.518 1147.309
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+ 619 TIM2e+G4 523.390 17 1080.780 1082.518 1147.309
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+ 639 TIM2e 523.390 16 1078.780 1080.321 1141.396
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+ 640 TIM2e+I 523.390 17 1080.780 1082.518 1147.309
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+ 641 TIM2e+G4 523.390 17 1080.780 1082.518 1147.309
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+ 661 TIM2 523.390 16 1078.780 1080.321 1141.396
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+ 662 TIM2+I 523.390 17 1080.780 1082.518 1147.309
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+ 663 TIM2+G4 523.390 17 1080.780 1082.518 1147.309
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  683 TIM2+F 519.933 19 1077.866 1080.037 1152.222
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  684 TIM2+F+I 519.933 20 1079.866 1082.273 1158.136
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  685 TIM2+F+G4 519.933 20 1079.866 1082.273 1158.136
@@ -161,8 +161,8 @@ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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  749 TIM3 523.262 16 1078.523 1080.064 1141.139
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  750 TIM3+I 523.262 17 1080.523 1082.262 1147.053
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  751 TIM3+G4 523.262 17 1080.523 1082.262 1147.053
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- 771 TIM3+F 519.669 19 1077.338 1079.510 1151.695
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- 772 TIM3+F+I 519.669 20 1079.338 1081.745 1157.608
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+ 771 TIM3+F 519.670 19 1077.339 1079.511 1151.696
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+ 772 TIM3+F+I 519.669 20 1079.339 1081.746 1157.609
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  773 TIM3+F+G4 519.669 20 1079.339 1081.746 1157.609
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  793 TVMe 523.261 17 1080.522 1082.261 1147.052
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  794 TVMe+I 523.261 18 1082.522 1084.471 1152.965
@@ -173,9 +173,9 @@ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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  837 TVM 523.261 17 1080.522 1082.261 1147.052
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  838 TVM+I 523.261 18 1082.522 1084.471 1152.965
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  839 TVM+G4 523.261 18 1082.522 1084.471 1152.965
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- 859 TVM+F 519.650 20 1079.299 1081.706 1157.569
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- 860 TVM+F+I 519.650 21 1081.299 1083.954 1163.483
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- 861 TVM+F+G4 519.650 21 1081.299 1083.954 1163.483
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+ 859 TVM+F 519.650 20 1079.300 1081.707 1157.570
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+ 860 TVM+F+I 519.650 21 1081.300 1083.955 1163.483
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+ 861 TVM+F+G4 519.650 21 1081.300 1083.955 1163.483
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  881 SYM 522.627 18 1081.254 1083.203 1151.697
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  882 SYM+I 522.627 19 1083.254 1085.425 1157.611
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  883 SYM+G4 522.627 19 1083.254 1085.425 1157.611
@@ -185,8 +185,8 @@ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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  925 GTR 522.627 18 1081.254 1083.203 1151.697
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  926 GTR+I 522.627 19 1083.254 1085.425 1157.611
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  927 GTR+G4 522.627 19 1083.254 1085.425 1157.611
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- 947 GTR+F 519.077 21 1080.154 1082.809 1162.338
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- 948 GTR+F+I 519.077 22 1082.154 1085.070 1168.251
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+ 947 GTR+F 519.077 21 1080.154 1082.810 1162.338
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+ 948 GTR+F+I 519.077 22 1082.154 1085.071 1168.251
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  949 GTR+F+G4 519.077 22 1082.154 1085.071 1168.251
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  Akaike Information Criterion: F81+F
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  Corrected Akaike Information Criterion: F81+F
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  Best-fit model: F81 chosen according to BIC
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  All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz
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- CPU time for ModelFinder: 0.084 seconds (0h:0m:0s)
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- Wall-clock time for ModelFinder: 0.092 seconds (0h:0m:0s)
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+ CPU time for ModelFinder: 0.115 seconds (0h:0m:0s)
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+ Wall-clock time for ModelFinder: 0.130 seconds (0h:0m:0s)
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  Estimate model parameters (epsilon = 0.100)
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  Parameters optimization took 1 rounds (0.000 sec)
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  Wrote distance file to...
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  Computing ML distances based on estimated model parameters...
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- Computing ML distances took 0.000082 sec (of wall-clock time) 0.000076 sec (of CPU time)
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- Constructing RapidNJ tree: done in 3.177e-05 secs using 88.13% CPU
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- Computing RapidNJ tree took 0.000079 sec (of wall-clock time) 0.000070 sec (of CPU time)
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+ Calculating distance matrix: done in 0.000120125 secs using 99.06% CPU
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+ Computing ML distances took 0.000137 sec (of wall-clock time) 0.000140 sec (of CPU time)
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+ Setting up auxiliary I and S matrices: done in 2.6339e-05 secs using 83.53% CPU
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+ Constructing RapidNJ tree: done in 4.2149e-05 secs using 85.41% CPU
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+ Computing RapidNJ tree took 0.000090 sec (of wall-clock time) 0.000078 sec (of CPU time)
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  Log-likelihood of RapidNJ tree: -521.220
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  --------------------------------------------------------------------
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  | INITIALIZING CANDIDATE TREE SET |
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- Computing log-likelihood of 98 initial trees ... 0.006 seconds
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+ Generating 98 parsimony trees... 0.011 second
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+ Computing log-likelihood of 98 initial trees ... 0.011 seconds
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  Current best score: -521.218
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- Optimizing NNI: done in 0.000150063 secs using 89.96% CPU
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+ Optimizing NNI: done in 0.000176579 secs using 87.78% CPU
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  Estimate model parameters (epsilon = 0.100)
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  Iteration 20 / LogL: -521.218 / Time: 0h:0m:0s
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  Finish initializing candidate tree set (20)
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- Current best tree score: -521.218 / CPU time: 0.019
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+ Current best tree score: -521.218 / CPU time: 0.028
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  Number of iterations: 20
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  --------------------------------------------------------------------
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  | OPTIMIZING CANDIDATE TREE SET |
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  Iteration 30 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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- BETTER TREE FOUND at iteration 38: -521.218
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- Iteration 130 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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- Optimizing NNI: done in 0.000147388 secs
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- Optimizing NNI: done in 0.000133251 secs
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- Optimizing NNI: done in 0.000105278 secs
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- Optimizing NNI: done in 0.000132419 secs
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- Optimizing NNI: done in 0.000143651 secs
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- Optimizing NNI: done in 0.000103726 secs
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- Optimizing NNI: done in 0.00013237 secs
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- Optimizing NNI: done in 0.000134664 secs
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- Optimizing NNI: done in 0.000133742 secs using 15.7% CPU
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- TREE SEARCH COMPLETED AFTER 139 ITERATIONS / Time: 0h:0m:0s
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+ Optimizing NNI: done in 0.000180217 secs using 98.77% CPU
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+ Optimizing NNI: done in 0.000156411 secs using 99.1% CPU
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+ TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
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  --------------------------------------------------------------------
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  | FINALIZING TREE SEARCH |
@@ -397,11 +356,11 @@ BEST SCORE FOUND : -521.218
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  Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.state
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  Total tree length: 0.005
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- Total number of iterations: 139
401
- CPU time used for tree search: 0.056 sec (0h:0m:0s)
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- Wall-clock time used for tree search: 0.053 sec (0h:0m:0s)
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- Total CPU time used: 0.148 sec (0h:0m:0s)
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- Total wall-clock time used: 0.157 sec (0h:0m:0s)
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+ Total number of iterations: 102
360
+ CPU time used for tree search: 0.063 sec (0h:0m:0s)
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+ Wall-clock time used for tree search: 0.060 sec (0h:0m:0s)
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+ Total CPU time used: 0.191 sec (0h:0m:0s)
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+ Total wall-clock time used: 0.205 sec (0h:0m:0s)
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  Analysis results written to:
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  IQ-TREE report: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree
@@ -410,4 +369,4 @@ Analysis results written to:
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  Ancestral state: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.state
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  Screen log file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.log
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- Date and Time: Sat Aug 16 23:08:16 2025
372
+ Date and Time: Mon Aug 18 15:31:52 2025