partis-bcr 1.0.8__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 (156) hide show
  1. packages/ham/bcrham +0 -0
  2. packages/ig-sw/src/ig_align/ig-sw +0 -0
  3. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +155 -73
  5. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  6. test/new-results/test.log +12 -16
  7. test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv +8 -8
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -1
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +8 -8
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -1
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +7 -7
  12. test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -1
  13. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +9 -9
  14. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
  15. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +8 -8
  16. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out +1 -1
  17. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +9 -9
  18. test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml +1 -1
  19. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out +1 -1
  20. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +8 -8
  21. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out +1 -1
  22. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +4 -4
  23. test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml +1 -1
  24. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
  25. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +9 -9
  26. test/paired/new-results/partition-new-simu/igh+igl/partition-igh-selection-metrics.yaml +1 -1
  27. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out +1 -1
  28. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +9 -9
  29. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/log +3 -3
  30. test/paired/new-results/partition-new-simu/igh+igl/partition-igl-selection-metrics.yaml +1 -1
  31. test/paired/new-results/partition-new-simu/selection-metrics.yaml +1 -1
  32. test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml +1 -1
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  37. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  38. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  39. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  40. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  41. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  42. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  43. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  44. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  45. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  46. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  47. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  48. test/paired/new-results/run-times.csv +6 -6
  49. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +86 -102
  50. test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml +1 -1
  51. test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml +1 -1
  52. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +84 -100
  53. test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml +1 -1
  54. test/paired/new-results/subset-partition-new-simu/merged-partition.log +50 -54
  55. test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igh.yaml +1 -1
  56. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  57. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  58. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  59. test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igh.yaml +1 -1
  60. test/paired/new-results/test.log +203 -236
  61. test/ref-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  62. test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  63. test/ref-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  64. test/ref-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  65. test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  66. test/ref-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  67. test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  68. test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  69. test/ref-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  70. test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa +24 -0
  71. test/ref-results/partition-new-simu/iqtree/iclust-0/log +430 -0
  72. test/ref-results/partition-new-simu/iqtree/iclust-0/out.bionj +1 -0
  73. test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
  74. test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +282 -0
  75. test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +429 -0
  76. test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist +13 -0
  77. test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
  78. test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +3529 -0
  79. test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -0
  80. test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa +16 -0
  81. test/ref-results/partition-new-simu/iqtree/iclust-1/log +373 -0
  82. test/ref-results/partition-new-simu/iqtree/iclust-1/out.bionj +1 -0
  83. test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
  84. test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +279 -0
  85. test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +372 -0
  86. test/ref-results/partition-new-simu/iqtree/iclust-1/out.mldist +9 -0
  87. test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
  88. test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +2229 -0
  89. test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -0
  90. test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa +16 -0
  91. test/ref-results/partition-new-simu/iqtree/iclust-2/log +375 -0
  92. test/ref-results/partition-new-simu/iqtree/iclust-2/out.bionj +1 -0
  93. test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
  94. test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +274 -0
  95. test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +374 -0
  96. test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist +9 -0
  97. test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
  98. test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +2283 -0
  99. test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -0
  100. test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -0
  101. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa +24 -0
  102. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +3461 -0
  103. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +10 -0
  104. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -0
  105. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -0
  106. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -0
  107. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  108. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +216 -0
  109. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -0
  110. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.rba +0 -0
  111. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy +9 -0
  112. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -0
  113. test/ref-results/partition-new-simu/raxml/iclust-0/log +454 -0
  114. test/ref-results/partition-new-simu/raxml/iclust-0/run.sh +3 -0
  115. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa +16 -0
  116. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralProbs +2203 -0
  117. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralStates +6 -0
  118. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -0
  119. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestModel +1 -0
  120. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -0
  121. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  122. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +217 -0
  123. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -0
  124. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.rba +0 -0
  125. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.reduced.phy +4 -0
  126. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -0
  127. test/ref-results/partition-new-simu/raxml/iclust-1/log +440 -0
  128. test/ref-results/partition-new-simu/raxml/iclust-1/run.sh +3 -0
  129. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa +16 -0
  130. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +2275 -0
  131. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -0
  132. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -0
  133. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -0
  134. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -0
  135. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  136. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +207 -0
  137. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -0
  138. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.rba +0 -0
  139. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -0
  140. test/ref-results/partition-new-simu/raxml/iclust-2/log +420 -0
  141. test/ref-results/partition-new-simu/raxml/iclust-2/run.sh +3 -0
  142. test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -0
  143. bin/FastTree-macos +0 -0
  144. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  145. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  146. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  147. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  148. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
  149. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  150. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
  151. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
  152. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
  153. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
  154. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
  155. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
  156. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree ADDED
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+ IQ-TREE 3.0.1 built May 5 2025
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+
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+ Input file name: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa
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+ Type of analysis: ModelFinder + tree reconstruction
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+ Random seed number: 801199
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+
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+ REFERENCES
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+ ----------
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+
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+ To cite IQ-TREE 3 please use:
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+
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+ Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Banos, Andrew J. Roger,
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+ Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn,
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+ Gavin Huttley, Robert Lanfear, Bui Quang Minh (2025)
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+ IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models.
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+ Submitted.
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+
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+ Please also cite the following paper(s) for the feature(s) that you used:
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+
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+ To cite ModelFinder please use:
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+
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+ Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
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+ and Lars S Jermiin (2017) ModelFinder: Fast model selection for
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+ accurate phylogenetic estimates. Nature Methods, 14:587–589.
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+ https://doi.org/10.1038/nmeth.4285
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+
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+ SEQUENCE ALIGNMENT
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+ ------------------
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+
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+ Input data: 8 sequences with 379 nucleotide sites
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+ Number of constant sites: 358 (= 94.4591% of all sites)
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+ Number of invariant (constant or ambiguous constant) sites: 358 (= 94.4591% of all sites)
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+ Number of parsimony informative sites: 4
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+ Number of distinct site patterns: 21
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+
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+ ModelFinder
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+ -----------
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+
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+ Best-fit model according to BIC: JC
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+
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+ List of models sorted by BIC scores:
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+
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+ Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
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+ JC -674.481 1374.962 - 0.0283 1375.959 - 0.0368 1426.150 + 0.277
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+ JC -674.481 1374.962 - 0.0283 1375.959 - 0.0368 1426.150 + 0.277
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+ F81 -674.481 1374.962 - 0.0283 1375.959 - 0.0368 1426.150 + 0.277
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+ HKY -674.481 1376.962 - 0.0104 1378.116 - 0.0125 1432.087 - 0.0142
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+ K2P -674.481 1376.962 - 0.0104 1378.116 - 0.0125 1432.087 - 0.0142
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+ K2P -674.481 1376.962 - 0.0104 1378.116 - 0.0125 1432.087 - 0.0142
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+ JC+I -674.481 1376.962 - 0.0104 1378.116 - 0.0125 1432.088 - 0.0142
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+ JC+I -674.481 1376.962 - 0.0104 1378.116 - 0.0125 1432.088 - 0.0142
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+ F81+I -674.481 1376.962 - 0.0104 1378.116 - 0.0125 1432.088 - 0.0142
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+ JC+G4 -674.481 1376.963 - 0.0104 1378.117 - 0.0125 1432.088 - 0.0142
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+ JC+G4 -674.481 1376.963 - 0.0104 1378.117 - 0.0125 1432.088 - 0.0142
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+ F81+G4 -674.481 1376.963 - 0.0104 1378.117 - 0.0125 1432.088 - 0.0142
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+ TN -672.458 1374.916 - 0.029 1376.238 - 0.032 1433.979 - 0.00553
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+ TNe -672.458 1374.916 - 0.029 1376.238 - 0.032 1433.979 - 0.00553
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+ TNe -672.458 1374.916 - 0.029 1376.238 - 0.032 1433.979 - 0.00553
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+ TPM2u -673.519 1377.038 - 0.01 1378.360 - 0.0111 1436.101 - 0.00191
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+ TPM2 -673.519 1377.038 - 0.01 1378.360 - 0.0111 1436.101 - 0.00191
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+ TPM2 -673.519 1377.038 - 0.01 1378.360 - 0.0111 1436.101 - 0.00191
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+ K3Pu -674.338 1378.676 - 0.00443 1379.998 - 0.00489 1437.739 - 0.000843
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+ K3P -674.338 1378.676 - 0.00443 1379.998 - 0.00489 1437.739 - 0.000843
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+ K3P -674.338 1378.676 - 0.00443 1379.998 - 0.00489 1437.739 - 0.000843
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+ TPM3u -674.438 1378.876 - 0.004 1380.199 - 0.00442 1437.940 - 0.000763
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+ TPM3 -674.438 1378.877 - 0.004 1380.199 - 0.00442 1437.940 - 0.000763
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+ TPM3 -674.438 1378.877 - 0.004 1380.199 - 0.00442 1437.940 - 0.000763
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+ F81+F -671.490 1374.980 - 0.0281 1376.482 - 0.0284 1437.980 - 0.000747
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+ TIM2 -671.494 1374.988 - 0.028 1376.491 - 0.0282 1437.988 - 0.000744
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+ TIM2e -671.494 1374.988 - 0.028 1376.491 - 0.0282 1437.988 - 0.000744
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+ TIM2e -671.494 1374.988 - 0.028 1376.491 - 0.0282 1437.988 - 0.000744
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+ HKY+I -674.481 1378.962 - 0.00384 1380.284 - 0.00424 1438.025 - 0.000731
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+ K2P+I -674.481 1378.962 - 0.00384 1380.284 - 0.00424 1438.025 - 0.000731
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+ K2P+I -674.481 1378.962 - 0.00384 1380.284 - 0.00424 1438.025 - 0.000731
75
+ JC+R2 -674.481 1378.963 - 0.00384 1380.285 - 0.00424 1438.026 - 0.000731
76
+ HKY+G4 -674.481 1378.963 - 0.00384 1380.285 - 0.00423 1438.026 - 0.000731
77
+ K2P+G4 -674.481 1378.963 - 0.00384 1380.285 - 0.00423 1438.026 - 0.000731
78
+ K2P+G4 -674.481 1378.963 - 0.00384 1380.285 - 0.00423 1438.026 - 0.000731
79
+ JC+I+G4 -674.940 1379.879 - 0.00243 1381.201 - 0.00268 1438.942 - 0.000462
80
+ TIM -672.315 1376.630 - 0.0123 1378.133 - 0.0124 1439.630 - 0.000328
81
+ TIMe -672.315 1376.630 - 0.0123 1378.133 - 0.0124 1439.630 - 0.000328
82
+ TIMe -672.315 1376.630 - 0.0123 1378.133 - 0.0124 1439.630 - 0.000328
83
+ TIM3 -672.415 1376.831 - 0.0111 1378.333 - 0.0112 1439.831 - 0.000296
84
+ TIM3e -672.415 1376.831 - 0.0111 1378.333 - 0.0112 1439.831 - 0.000296
85
+ TIM3e -672.415 1376.831 - 0.0111 1378.333 - 0.0112 1439.831 - 0.000296
86
+ TN+I -672.458 1376.916 - 0.0107 1378.419 - 0.0108 1439.917 - 0.000284
87
+ TNe+I -672.458 1376.916 - 0.0107 1378.419 - 0.0108 1439.917 - 0.000284
88
+ TNe+I -672.458 1376.916 - 0.0107 1378.419 - 0.0108 1439.917 - 0.000284
89
+ TN+G4 -672.458 1376.917 - 0.0107 1378.420 - 0.0108 1439.917 - 0.000284
90
+ TNe+G4 -672.458 1376.917 - 0.0107 1378.420 - 0.0108 1439.917 - 0.000284
91
+ TNe+G4 -672.458 1376.917 - 0.0107 1378.420 - 0.0108 1439.917 - 0.000284
92
+ TPM2u+I -673.519 1379.038 - 0.00369 1380.541 - 0.00373 1442.038 - 9.83e-05
93
+ TPM2+I -673.519 1379.038 - 0.00369 1380.541 - 0.00373 1442.039 - 9.82e-05
94
+ TPM2+I -673.519 1379.038 - 0.00369 1380.541 - 0.00373 1442.039 - 9.82e-05
95
+ TPM2u+G4 -673.519 1379.039 - 0.00369 1380.542 - 0.00373 1442.039 - 9.82e-05
96
+ TPM2+G4 -673.519 1379.039 - 0.00369 1380.542 - 0.00373 1442.039 - 9.82e-05
97
+ TPM2+G4 -673.519 1379.039 - 0.00369 1380.542 - 0.00373 1442.039 - 9.82e-05
98
+ K3Pu+I -674.338 1380.676 - 0.00163 1382.179 - 0.00164 1443.676 - 4.33e-05
99
+ K3P+I -674.338 1380.676 - 0.00163 1382.179 - 0.00164 1443.676 - 4.33e-05
100
+ K3P+I -674.338 1380.676 - 0.00163 1382.179 - 0.00164 1443.676 - 4.33e-05
101
+ K3Pu+G4 -674.338 1380.677 - 0.00163 1382.179 - 0.00164 1443.677 - 4.33e-05
102
+ K3P+G4 -674.338 1380.677 - 0.00163 1382.179 - 0.00164 1443.677 - 4.33e-05
103
+ K3P+G4 -674.338 1380.677 - 0.00163 1382.179 - 0.00164 1443.677 - 4.33e-05
104
+ TPM3u+I -674.438 1380.876 - 0.00147 1382.379 - 0.00149 1443.877 - 3.92e-05
105
+ TPM3+I -674.438 1380.877 - 0.00147 1382.379 - 0.00149 1443.877 - 3.92e-05
106
+ TPM3+I -674.438 1380.877 - 0.00147 1382.379 - 0.00149 1443.877 - 3.92e-05
107
+ TPM3u+G4 -674.439 1380.877 - 0.00147 1382.380 - 0.00149 1443.878 - 3.92e-05
108
+ TPM3+G4 -674.439 1380.877 - 0.00147 1382.380 - 0.00149 1443.878 - 3.92e-05
109
+ TPM3+G4 -674.439 1380.877 - 0.00147 1382.380 - 0.00149 1443.878 - 3.92e-05
110
+ HKY+F -671.489 1376.977 - 0.0103 1378.673 - 0.00948 1443.916 - 3.84e-05
111
+ F81+F+I -671.490 1376.980 - 0.0103 1378.675 - 0.00947 1443.918 - 3.84e-05
112
+ F81+F+G4 -671.490 1376.980 - 0.0103 1378.676 - 0.00947 1443.918 - 3.84e-05
113
+ TIM2+I -671.494 1376.988 - 0.0103 1378.683 - 0.00943 1443.926 - 3.82e-05
114
+ TIM2e+I -671.494 1376.988 - 0.0103 1378.683 - 0.00943 1443.926 - 3.82e-05
115
+ TIM2e+I -671.494 1376.988 - 0.0103 1378.683 - 0.00943 1443.926 - 3.82e-05
116
+ TIM2+G4 -671.494 1376.989 - 0.0103 1378.684 - 0.00943 1443.927 - 3.82e-05
117
+ TIM2e+G4 -671.494 1376.989 - 0.0103 1378.684 - 0.00943 1443.927 - 3.82e-05
118
+ TIM2e+G4 -671.494 1376.989 - 0.0103 1378.684 - 0.00943 1443.927 - 3.82e-05
119
+ JC+I+R2 -674.942 1381.884 - 0.00089 1383.386 - 0.000898 1444.884 - 2.37e-05
120
+ TIM+I -672.315 1378.630 - 0.00453 1380.325 - 0.00415 1445.568 - 1.68e-05
121
+ TIMe+I -672.315 1378.630 - 0.00453 1380.325 - 0.00415 1445.568 - 1.68e-05
122
+ TIMe+I -672.315 1378.630 - 0.00453 1380.325 - 0.00415 1445.568 - 1.68e-05
123
+ TIM+G4 -672.315 1378.631 - 0.00453 1380.326 - 0.00415 1445.569 - 1.68e-05
124
+ TIMe+G4 -672.315 1378.631 - 0.00453 1380.326 - 0.00415 1445.569 - 1.68e-05
125
+ TIMe+G4 -672.315 1378.631 - 0.00453 1380.326 - 0.00415 1445.569 - 1.68e-05
126
+ TN+F -669.425 1374.851 - 0.03 1376.751 - 0.0248 1445.726 - 1.55e-05
127
+ TIM3+I -672.415 1378.831 - 0.0041 1380.526 - 0.00375 1445.769 - 1.52e-05
128
+ TIM3e+I -672.415 1378.831 - 0.0041 1380.526 - 0.00375 1445.769 - 1.52e-05
129
+ TIM3e+I -672.415 1378.831 - 0.0041 1380.526 - 0.00375 1445.769 - 1.52e-05
130
+ TIM3+G4 -672.416 1378.832 - 0.0041 1380.527 - 0.00375 1445.770 - 1.52e-05
131
+ TIM3e+G4 -672.416 1378.832 - 0.0041 1380.527 - 0.00375 1445.770 - 1.52e-05
132
+ TIM3e+G4 -672.416 1378.832 - 0.0041 1380.527 - 0.00375 1445.770 - 1.52e-05
133
+ TVM -673.109 1380.218 - 0.00205 1381.914 - 0.00188 1447.156 - 7.6e-06
134
+ TVMe -673.109 1380.218 - 0.00205 1381.914 - 0.00188 1447.157 - 7.6e-06
135
+ TVMe -673.109 1380.218 - 0.00205 1381.914 - 0.00188 1447.157 - 7.6e-06
136
+ TPM2u+F -670.831 1377.663 - 0.00735 1379.563 - 0.00608 1448.539 - 3.81e-06
137
+ GTR -671.084 1378.168 - 0.00571 1380.068 - 0.00472 1449.043 - 2.96e-06
138
+ SYM -671.084 1378.168 - 0.00571 1380.068 - 0.00472 1449.043 - 2.96e-06
139
+ SYM -671.084 1378.168 - 0.00571 1380.068 - 0.00472 1449.043 - 2.96e-06
140
+ K3Pu+F -671.310 1378.621 - 0.00455 1380.521 - 0.00376 1449.496 - 2.36e-06
141
+ TPM3u+F -671.487 1378.975 - 0.00381 1380.875 - 0.00315 1449.851 - 1.98e-06
142
+ HKY+F+I -671.489 1378.977 - 0.00381 1380.877 - 0.00315 1449.853 - 1.97e-06
143
+ HKY+F+G4 -671.489 1378.978 - 0.00381 1380.878 - 0.00315 1449.854 - 1.97e-06
144
+ JC+R3 -674.481 1382.962 - 0.000519 1384.658 - 0.000476 1449.900 - 1.93e-06
145
+ TIM2+F -668.767 1375.534 - 0.0213 1377.651 - 0.0158 1450.348 - 1.54e-06
146
+ TIM+F -669.247 1376.494 - 0.0132 1378.611 - 0.00978 1451.307 - 9.54e-07
147
+ TIM3+F -669.424 1376.849 - 0.011 1378.966 - 0.00819 1451.662 - 7.99e-07
148
+ TN+F+I -669.425 1376.851 - 0.011 1378.968 - 0.00818 1451.664 - 7.98e-07
149
+ TN+F+G4 -669.426 1376.852 - 0.011 1378.969 - 0.00818 1451.665 - 7.98e-07
150
+ TVM+I -673.109 1382.218 - 0.000753 1384.118 - 0.000623 1453.094 - 3.91e-07
151
+ TVMe+I -673.109 1382.218 - 0.000753 1384.118 - 0.000623 1453.094 - 3.91e-07
152
+ TVMe+I -673.109 1382.218 - 0.000753 1384.118 - 0.000623 1453.094 - 3.91e-07
153
+ TVM+G4 -673.109 1382.219 - 0.000753 1384.119 - 0.000623 1453.095 - 3.9e-07
154
+ TVMe+G4 -673.110 1382.219 - 0.000753 1384.119 - 0.000623 1453.095 - 3.9e-07
155
+ TVMe+G4 -673.110 1382.219 - 0.000753 1384.119 - 0.000623 1453.095 - 3.9e-07
156
+ TPM2u+F+I -670.831 1379.663 - 0.0027 1381.780 - 0.00201 1454.476 - 1.96e-07
157
+ TPM2u+F+G4 -670.832 1379.664 - 0.0027 1381.781 - 0.002 1454.477 - 1.96e-07
158
+ GTR+I -671.084 1380.168 - 0.0021 1382.285 - 0.00156 1454.981 - 1.52e-07
159
+ SYM+I -671.084 1380.168 - 0.0021 1382.285 - 0.00156 1454.981 - 1.52e-07
160
+ SYM+I -671.084 1380.168 - 0.0021 1382.285 - 0.00156 1454.981 - 1.52e-07
161
+ GTR+G4 -671.084 1380.169 - 0.0021 1382.286 - 0.00156 1454.982 - 1.52e-07
162
+ SYM+G4 -671.084 1380.169 - 0.0021 1382.286 - 0.00156 1454.982 - 1.52e-07
163
+ SYM+G4 -671.084 1380.169 - 0.0021 1382.286 - 0.00156 1454.982 - 1.52e-07
164
+ K3Pu+F+I -671.310 1380.620 - 0.00167 1382.737 - 0.00124 1455.433 - 1.21e-07
165
+ K3Pu+F+G4 -671.311 1380.621 - 0.00167 1382.738 - 0.00124 1455.434 - 1.21e-07
166
+ TPM3u+F+I -671.487 1380.975 - 0.0014 1383.092 - 0.00104 1455.788 - 1.02e-07
167
+ TPM3u+F+G4 -671.488 1380.975 - 0.0014 1383.092 - 0.00104 1455.789 - 1.02e-07
168
+ TIM2+F+I -668.767 1377.534 - 0.00783 1379.881 - 0.00518 1456.285 - 7.92e-08
169
+ TIM2+F+G4 -668.768 1377.535 - 0.00783 1379.882 - 0.00518 1456.286 - 7.92e-08
170
+ JC+I+R3 -674.935 1385.870 - 0.000121 1387.770 - 0.0001 1456.746 - 6.29e-08
171
+ TIM+F+I -669.247 1378.494 - 0.00485 1380.840 - 0.00321 1457.245 - 4.9e-08
172
+ TIM+F+G4 -669.247 1378.495 - 0.00485 1380.841 - 0.00321 1457.246 - 4.9e-08
173
+ TIM3+F+I -669.424 1378.849 - 0.00406 1381.195 - 0.00269 1457.599 - 4.11e-08
174
+ TIM3+F+G4 -669.425 1378.850 - 0.00406 1381.196 - 0.00269 1457.600 - 4.1e-08
175
+ TVM+F -670.452 1380.904 - 0.00145 1383.251 - 0.000961 1459.655 - 1.47e-08
176
+ GTR+F -668.388 1378.775 - 0.00421 1381.363 - 0.00247 1461.463 - 5.95e-09
177
+ TVM+F+I -670.452 1382.904 - 0.000534 1385.493 - 0.000313 1465.593 - 7.54e-10
178
+ TVM+F+G4 -670.453 1382.905 - 0.000534 1385.493 - 0.000313 1465.593 - 7.54e-10
179
+ GTR+F+I -668.388 1380.775 - 0.00155 1383.618 - 0.0008 1467.401 - 3.05e-10
180
+ GTR+F+G4 -668.388 1380.776 - 0.00155 1383.619 - 0.0008 1467.402 - 3.05e-10
181
+
182
+ AIC, w-AIC : Akaike information criterion scores and weights.
183
+ AICc, w-AICc : Corrected AIC scores and weights.
184
+ BIC, w-BIC : Bayesian information criterion scores and weights.
185
+
186
+ Plus signs denote the 95% confidence sets.
187
+ Minus signs denote significant exclusion.
188
+
189
+ SUBSTITUTION PROCESS
190
+ --------------------
191
+
192
+ Model of substitution: JC
193
+
194
+ Rate parameter R:
195
+
196
+ A-C: 1.0000
197
+ A-G: 1.0000
198
+ A-T: 1.0000
199
+ C-G: 1.0000
200
+ C-T: 1.0000
201
+ G-T: 1.0000
202
+
203
+ State frequencies: (equal frequencies)
204
+
205
+ Rate matrix Q:
206
+
207
+ A -1 0.3333 0.3333 0.3333
208
+ C 0.3333 -1 0.3333 0.3333
209
+ G 0.3333 0.3333 -1 0.3333
210
+ T 0.3333 0.3333 0.3333 -1
211
+
212
+ Model of rate heterogeneity: Uniform
213
+
214
+ MAXIMUM LIKELIHOOD TREE
215
+ -----------------------
216
+
217
+ Log-likelihood of the tree: -674.4810 (s.e. 27.3364)
218
+ Unconstrained log-likelihood (without tree): -633.4529
219
+ Number of free parameters (#branches + #model parameters): 13
220
+ Akaike information criterion (AIC) score: 1374.9620
221
+ Corrected Akaike information criterion (AICc) score: 1375.9593
222
+ Bayesian information criterion (BIC) score: 1426.1500
223
+
224
+ Total tree length (sum of branch lengths): 0.0557
225
+ Sum of internal branch lengths: 0.0106 (19.0068% of tree length)
226
+
227
+ WARNING: 2 near-zero internal branches (<0.0026) should be treated with caution
228
+ Such branches are denoted by '**' in the figure below
229
+
230
+ NOTE: Tree is UNROOTED although outgroup taxon 'XnaiveX' is drawn at root
231
+
232
+ +--------XnaiveX
233
+ | (Node1)
234
+ | +------------------162cb1691f
235
+ | +------------------| (Node4)
236
+ | | +--------17f57acf2e
237
+ | +--------| (Node3)
238
+ | | | +------------------73431a9b10
239
+ | | | +--------| (Node6)
240
+ | | | | +**bf50fa2017
241
+ | | +**| (Node5)
242
+ | | +------------------948b83fb4d
243
+ +**| (Node2)
244
+ | +----------------------------73d6c6e558
245
+ |
246
+ +-----------------------------------------------------------c8a90cc3d7
247
+
248
+ Tree in newick format:
249
+
250
+ (XnaiveX:0.0026431745,(((162cb1691f:0.0053051714,17f57acf2e:0.0026431546)Node4:0.0053051782,((73431a9b10:0.0052956972,bf50fa2017:0.0000010000)Node6:0.0026431789,948b83fb4d:0.0052957106)Node5:0.0000010000)Node3:0.0026431908,73d6c6e558:0.0079576343)Node2:0.0000010000,c8a90cc3d7:0.0160006069)Node1;
251
+
252
+ ALISIM COMMAND
253
+ --------------
254
+ To simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis, you can use the following command:
255
+
256
+ --alisim simulated_MSA -t /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile -m "JC" --length 379
257
+
258
+ To mimic the alignment used to produce this analysis, i.e. simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis *and* copying the same gap positions as the original alignment, you can use the following command:
259
+
260
+ iqtree -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa --alisim mimicked_MSA
261
+
262
+ To simulate any number of alignments in either of the two commandlines above, use the --num-alignments options, for example mimic 100 alignments you would use the command line:
263
+
264
+ iqtree -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa --alisim mimicked_MSA --num-alignments 100
265
+
266
+ For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim
267
+
268
+ TIME STAMP
269
+ ----------
270
+
271
+ Date and time: Mon Aug 18 15:31:52 2025
272
+ Total CPU time used: 0.153605 seconds (0h:0m:0s)
273
+ Total wall-clock time used: 0.170284 seconds (0h:0m:0s)
274
+
test/ref-results/partition-new-simu/iqtree/iclust-2/out.log ADDED
@@ -0,0 +1,374 @@
1
+ IQ-TREE version 3.0.1 for Linux x86 64-bit built May 5 2025
2
+ Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
3
+ Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow,
4
+ Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt
5
+
6
+ Host: pkrvmubgrv54qmi (AVX2, FMA3, 15 GB RAM)
7
+ Command: /home/runner/work/partis/partis/bin/iqtree3_intel -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out -o XnaiveX
8
+ Seed: 801199 (Using SPRNG - Scalable Parallel Random Number Generator)
9
+ Time: Mon Aug 18 15:31:52 2025
10
+ Kernel: AVX+FMA - 1 threads (4 CPU cores detected)
11
+
12
+ HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
13
+ HINT: -nt AUTO will automatically determine the best number of threads to use.
14
+
15
+ Reading alignment file /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa ... Fasta format detected
16
+ Reading fasta file: done in 7.8927e-05 secs using 98.83% CPU
17
+ Alignment most likely contains DNA/RNA sequences
18
+ Constructing alignment: done in 0.000400938 secs using 36.17% CPU
19
+ Alignment has 8 sequences with 379 columns, 21 distinct patterns
20
+ 4 parsimony-informative, 17 singleton sites, 358 constant sites
21
+ Gap/Ambiguity Composition p-value
22
+ Analyzing sequences: done in 8.516e-06 secs
23
+ 1 XnaiveX 0.00% passed 99.90%
24
+ 2 162cb1691f 0.00% passed 99.94%
25
+ 3 17f57acf2e 0.00% passed 99.94%
26
+ 4 73431a9b10 0.00% passed 99.81%
27
+ 5 73d6c6e558 0.00% passed 98.68%
28
+ 6 948b83fb4d 0.00% passed 99.88%
29
+ 7 bf50fa2017 0.00% passed 99.81%
30
+ 8 c8a90cc3d7 0.00% passed 99.56%
31
+ **** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=3)
32
+
33
+
34
+ Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
35
+ Perform fast likelihood tree search using GTR+I+G model...
36
+ Estimate model parameters (epsilon = 5.000)
37
+ Perform nearest neighbor interchange...
38
+ Optimizing NNI: done in 0.000480928 secs using 93.36% CPU
39
+ Estimate model parameters (epsilon = 1.000)
40
+ 1. Initial log-likelihood: -668.906
41
+ Optimal log-likelihood: -668.900
42
+ Rate parameters: A-C: 0.58043 A-G: 0.19277 A-T: 0.25950 C-G: 0.74204 C-T: 1.19039 G-T: 1.00000
43
+ Base frequencies: A: 0.219 C: 0.280 G: 0.285 T: 0.216
44
+ Proportion of invariable sites: 0.470
45
+ Gamma shape alpha: 998.448
46
+ Parameters optimization took 1 rounds (0.001 sec)
47
+ Time for fast ML tree search: 0.004 seconds
48
+
49
+ NOTE: ModelFinder requires 0 MB RAM!
50
+ ModelFinder will test up to 968 DNA models (sample size: 379 epsilon: 0.100) ...
51
+ No. Model -LnL df AIC AICc BIC
52
+ 1 JC 674.481 13 1374.962 1375.959 1426.150
53
+ 2 JC+I 674.481 14 1376.962 1378.116 1432.088
54
+ 3 JC+G4 674.481 14 1376.963 1378.117 1432.088
55
+ 4 JC+I+G4 674.940 15 1379.879 1381.201 1438.942
56
+ 5 JC+R2 674.481 15 1378.963 1380.285 1438.026
57
+ 6 JC+R3 674.481 17 1382.962 1384.658 1449.900
58
+ 14 JC+I+R2 674.942 16 1381.884 1383.386 1444.884
59
+ 15 JC+I+R3 674.935 18 1385.870 1387.770 1456.746
60
+ 23 JC 674.481 13 1374.962 1375.959 1426.150
61
+ 24 JC+I 674.481 14 1376.962 1378.116 1432.088
62
+ 25 JC+G4 674.481 14 1376.963 1378.117 1432.088
63
+ 45 F81 674.481 13 1374.962 1375.959 1426.150
64
+ 46 F81+I 674.481 14 1376.962 1378.116 1432.088
65
+ 47 F81+G4 674.481 14 1376.963 1378.117 1432.088
66
+ 67 F81+F 671.490 16 1374.980 1376.482 1437.980
67
+ 68 F81+F+I 671.490 17 1376.980 1378.675 1443.918
68
+ 69 F81+F+G4 671.490 17 1376.980 1378.676 1443.918
69
+ 89 K2P 674.481 14 1376.962 1378.116 1432.087
70
+ 90 K2P+I 674.481 15 1378.962 1380.284 1438.025
71
+ 91 K2P+G4 674.481 15 1378.963 1380.285 1438.026
72
+ 111 K2P 674.481 14 1376.962 1378.116 1432.087
73
+ 112 K2P+I 674.481 15 1378.962 1380.284 1438.025
74
+ 113 K2P+G4 674.481 15 1378.963 1380.285 1438.026
75
+ 133 HKY 674.481 14 1376.962 1378.116 1432.087
76
+ 134 HKY+I 674.481 15 1378.962 1380.284 1438.025
77
+ 135 HKY+G4 674.481 15 1378.963 1380.285 1438.026
78
+ 155 HKY+F 671.489 17 1376.977 1378.673 1443.916
79
+ 156 HKY+F+I 671.489 18 1378.977 1380.877 1449.853
80
+ 157 HKY+F+G4 671.489 18 1378.978 1380.878 1449.854
81
+ 177 TNe 672.458 15 1374.916 1376.238 1433.979
82
+ 178 TNe+I 672.458 16 1376.916 1378.419 1439.917
83
+ 179 TNe+G4 672.458 16 1376.917 1378.420 1439.917
84
+ 199 TNe 672.458 15 1374.916 1376.238 1433.979
85
+ 200 TNe+I 672.458 16 1376.916 1378.419 1439.917
86
+ 201 TNe+G4 672.458 16 1376.917 1378.420 1439.917
87
+ 221 TN 672.458 15 1374.916 1376.238 1433.979
88
+ 222 TN+I 672.458 16 1376.916 1378.419 1439.917
89
+ 223 TN+G4 672.458 16 1376.917 1378.420 1439.917
90
+ 243 TN+F 669.425 18 1374.851 1376.751 1445.726
91
+ 244 TN+F+I 669.425 19 1376.851 1378.968 1451.664
92
+ 245 TN+F+G4 669.426 19 1376.852 1378.969 1451.665
93
+ 265 K3P 674.338 15 1378.676 1379.998 1437.739
94
+ 266 K3P+I 674.338 16 1380.676 1382.179 1443.676
95
+ 267 K3P+G4 674.338 16 1380.677 1382.179 1443.677
96
+ 287 K3P 674.338 15 1378.676 1379.998 1437.739
97
+ 288 K3P+I 674.338 16 1380.676 1382.179 1443.676
98
+ 289 K3P+G4 674.338 16 1380.677 1382.179 1443.677
99
+ 309 K3Pu 674.338 15 1378.676 1379.998 1437.739
100
+ 310 K3Pu+I 674.338 16 1380.676 1382.179 1443.676
101
+ 311 K3Pu+G4 674.338 16 1380.677 1382.179 1443.677
102
+ 331 K3Pu+F 671.310 18 1378.621 1380.521 1449.496
103
+ 332 K3Pu+F+I 671.310 19 1380.620 1382.737 1455.433
104
+ 333 K3Pu+F+G4 671.311 19 1380.621 1382.738 1455.434
105
+ 353 TPM2 673.519 15 1377.038 1378.360 1436.101
106
+ 354 TPM2+I 673.519 16 1379.038 1380.541 1442.039
107
+ 355 TPM2+G4 673.519 16 1379.039 1380.542 1442.039
108
+ 375 TPM2 673.519 15 1377.038 1378.360 1436.101
109
+ 376 TPM2+I 673.519 16 1379.038 1380.541 1442.039
110
+ 377 TPM2+G4 673.519 16 1379.039 1380.542 1442.039
111
+ 397 TPM2u 673.519 15 1377.038 1378.360 1436.101
112
+ 398 TPM2u+I 673.519 16 1379.038 1380.541 1442.038
113
+ 399 TPM2u+G4 673.519 16 1379.039 1380.542 1442.039
114
+ 419 TPM2u+F 670.831 18 1377.663 1379.563 1448.539
115
+ 420 TPM2u+F+I 670.831 19 1379.663 1381.780 1454.476
116
+ 421 TPM2u+F+G4 670.832 19 1379.664 1381.781 1454.477
117
+ 441 TPM3 674.438 15 1378.877 1380.199 1437.940
118
+ 442 TPM3+I 674.438 16 1380.877 1382.379 1443.877
119
+ 443 TPM3+G4 674.439 16 1380.877 1382.380 1443.878
120
+ 463 TPM3 674.438 15 1378.877 1380.199 1437.940
121
+ 464 TPM3+I 674.438 16 1380.877 1382.379 1443.877
122
+ 465 TPM3+G4 674.439 16 1380.877 1382.380 1443.878
123
+ 485 TPM3u 674.438 15 1378.876 1380.199 1437.940
124
+ 486 TPM3u+I 674.438 16 1380.876 1382.379 1443.877
125
+ 487 TPM3u+G4 674.439 16 1380.877 1382.380 1443.878
126
+ 507 TPM3u+F 671.487 18 1378.975 1380.875 1449.851
127
+ 508 TPM3u+F+I 671.487 19 1380.975 1383.092 1455.788
128
+ 509 TPM3u+F+G4 671.488 19 1380.975 1383.092 1455.789
129
+ 529 TIMe 672.315 16 1376.630 1378.133 1439.630
130
+ 530 TIMe+I 672.315 17 1378.630 1380.325 1445.568
131
+ 531 TIMe+G4 672.315 17 1378.631 1380.326 1445.569
132
+ 551 TIMe 672.315 16 1376.630 1378.133 1439.630
133
+ 552 TIMe+I 672.315 17 1378.630 1380.325 1445.568
134
+ 553 TIMe+G4 672.315 17 1378.631 1380.326 1445.569
135
+ 573 TIM 672.315 16 1376.630 1378.133 1439.630
136
+ 574 TIM+I 672.315 17 1378.630 1380.325 1445.568
137
+ 575 TIM+G4 672.315 17 1378.631 1380.326 1445.569
138
+ 595 TIM+F 669.247 19 1376.494 1378.611 1451.307
139
+ 596 TIM+F+I 669.247 20 1378.494 1380.840 1457.245
140
+ 597 TIM+F+G4 669.247 20 1378.495 1380.841 1457.246
141
+ 617 TIM2e 671.494 16 1374.988 1376.491 1437.988
142
+ 618 TIM2e+I 671.494 17 1376.988 1378.683 1443.926
143
+ 619 TIM2e+G4 671.494 17 1376.989 1378.684 1443.927
144
+ 639 TIM2e 671.494 16 1374.988 1376.491 1437.988
145
+ 640 TIM2e+I 671.494 17 1376.988 1378.683 1443.926
146
+ 641 TIM2e+G4 671.494 17 1376.989 1378.684 1443.927
147
+ 661 TIM2 671.494 16 1374.988 1376.491 1437.988
148
+ 662 TIM2+I 671.494 17 1376.988 1378.683 1443.926
149
+ 663 TIM2+G4 671.494 17 1376.989 1378.684 1443.927
150
+ 683 TIM2+F 668.767 19 1375.534 1377.651 1450.348
151
+ 684 TIM2+F+I 668.767 20 1377.534 1379.881 1456.285
152
+ 685 TIM2+F+G4 668.768 20 1377.535 1379.882 1456.286
153
+ 705 TIM3e 672.415 16 1376.831 1378.333 1439.831
154
+ 706 TIM3e+I 672.415 17 1378.831 1380.526 1445.769
155
+ 707 TIM3e+G4 672.416 17 1378.832 1380.527 1445.770
156
+ 727 TIM3e 672.415 16 1376.831 1378.333 1439.831
157
+ 728 TIM3e+I 672.415 17 1378.831 1380.526 1445.769
158
+ 729 TIM3e+G4 672.416 17 1378.832 1380.527 1445.770
159
+ 749 TIM3 672.415 16 1376.831 1378.333 1439.831
160
+ 750 TIM3+I 672.415 17 1378.831 1380.526 1445.769
161
+ 751 TIM3+G4 672.416 17 1378.832 1380.527 1445.770
162
+ 771 TIM3+F 669.424 19 1376.849 1378.966 1451.662
163
+ 772 TIM3+F+I 669.424 20 1378.849 1381.195 1457.599
164
+ 773 TIM3+F+G4 669.425 20 1378.850 1381.196 1457.600
165
+ 793 TVMe 673.109 17 1380.218 1381.914 1447.157
166
+ 794 TVMe+I 673.109 18 1382.218 1384.118 1453.094
167
+ 795 TVMe+G4 673.110 18 1382.219 1384.119 1453.095
168
+ 815 TVMe 673.109 17 1380.218 1381.914 1447.157
169
+ 816 TVMe+I 673.109 18 1382.218 1384.118 1453.094
170
+ 817 TVMe+G4 673.110 18 1382.219 1384.119 1453.095
171
+ 837 TVM 673.109 17 1380.218 1381.914 1447.156
172
+ 838 TVM+I 673.109 18 1382.218 1384.118 1453.094
173
+ 839 TVM+G4 673.109 18 1382.219 1384.119 1453.095
174
+ 859 TVM+F 670.452 20 1380.904 1383.251 1459.655
175
+ 860 TVM+F+I 670.452 21 1382.904 1385.493 1465.593
176
+ 861 TVM+F+G4 670.453 21 1382.905 1385.493 1465.593
177
+ 881 SYM 671.084 18 1378.168 1380.068 1449.043
178
+ 882 SYM+I 671.084 19 1380.168 1382.285 1454.981
179
+ 883 SYM+G4 671.084 19 1380.169 1382.286 1454.982
180
+ 903 SYM 671.084 18 1378.168 1380.068 1449.043
181
+ 904 SYM+I 671.084 19 1380.168 1382.285 1454.981
182
+ 905 SYM+G4 671.084 19 1380.169 1382.286 1454.982
183
+ 925 GTR 671.084 18 1378.168 1380.068 1449.043
184
+ 926 GTR+I 671.084 19 1380.168 1382.285 1454.981
185
+ 927 GTR+G4 671.084 19 1380.169 1382.286 1454.982
186
+ 947 GTR+F 668.388 21 1378.775 1381.363 1461.463
187
+ 948 GTR+F+I 668.388 22 1380.775 1383.618 1467.401
188
+ 949 GTR+F+G4 668.388 22 1380.776 1383.619 1467.402
189
+ Akaike Information Criterion: TN+F
190
+ Corrected Akaike Information Criterion: JC
191
+ Bayesian Information Criterion: JC
192
+ Best-fit model: JC chosen according to BIC
193
+
194
+ All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz
195
+ CPU time for ModelFinder: 0.066 seconds (0h:0m:0s)
196
+ Wall-clock time for ModelFinder: 0.075 seconds (0h:0m:0s)
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+
198
+ NOTE: 0 MB RAM (0 GB) is required!
199
+ Estimate model parameters (epsilon = 0.100)
200
+ 1. Initial log-likelihood: -674.481
201
+ Optimal log-likelihood: -674.481
202
+ 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
203
+ Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
204
+ Parameters optimization took 1 rounds (0.000 sec)
205
+ Wrote distance file to...
206
+ Computing ML distances based on estimated model parameters...
207
+ Calculating distance matrix: done in 0.000124302 secs using 89.3% CPU
208
+ Computing ML distances took 0.000140 sec (of wall-clock time) 0.000127 sec (of CPU time)
209
+ Setting up auxiliary I and S matrices: done in 2.667e-05 secs using 86.24% CPU
210
+ Constructing RapidNJ tree: done in 3.232e-05 secs using 86.63% CPU
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+ Computing RapidNJ tree took 0.000079 sec (of wall-clock time) 0.000071 sec (of CPU time)
212
+ Log-likelihood of RapidNJ tree: -680.247
213
+ --------------------------------------------------------------------
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+ | INITIALIZING CANDIDATE TREE SET |
215
+ --------------------------------------------------------------------
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+ Generating 98 parsimony trees... 0.015 second
217
+ Computing log-likelihood of 66 initial trees ... 0.005 seconds
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+ Current best score: -674.481
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+
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+ Do NNI search on 20 best initial trees
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+ Optimizing NNI: done in 0.000217055 secs using 90.76% CPU
222
+ Estimate model parameters (epsilon = 0.100)
223
+ BETTER TREE FOUND at iteration 1: -674.481
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+ Optimizing NNI: done in 0.000177983 secs
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+ Optimizing NNI: done in 0.000207597 secs
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+ Optimizing NNI: done in 0.000200935 secs
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+ Optimizing NNI: done in 0.000228316 secs using 91.1% CPU
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+ Optimizing NNI: done in 0.000206866 secs using 89.91% CPU
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+ Optimizing NNI: done in 0.000225581 secs using 89.99% CPU
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+ Optimizing NNI: done in 0.000206025 secs using 90.28% CPU
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+ Optimizing NNI: done in 0.000223937 secs using 99.58% CPU
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+ Optimizing NNI: done in 0.000442726 secs using 99.84% CPU
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+ Iteration 10 / LogL: -674.481 / Time: 0h:0m:0s
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+ Optimizing NNI: done in 0.000450561 secs
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+ Optimizing NNI: done in 0.000436274 secs
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+ Optimizing NNI: done in 0.000435944 secs using 51.38% CPU
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+ Optimizing NNI: done in 0.000434852 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000196477 secs using 99.25% CPU
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+ Optimizing NNI: done in 0.000475437 secs using 99.7% CPU
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+ Optimizing NNI: done in 0.000667235 secs using 99.96% CPU
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+ Optimizing NNI: done in 0.000832193 secs using 99.86% CPU
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+ Optimizing NNI: done in 0.000882326 secs using 99.85% CPU
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+ Optimizing NNI: done in 0.000560486 secs using 99.91% CPU
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+ Iteration 20 / LogL: -674.482 / Time: 0h:0m:0s
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+ Finish initializing candidate tree set (5)
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+ Current best tree score: -674.481 / CPU time: 0.029
247
+ Number of iterations: 20
248
+ --------------------------------------------------------------------
249
+ | OPTIMIZING CANDIDATE TREE SET |
250
+ --------------------------------------------------------------------
251
+ Optimizing NNI: done in 0.000679819 secs using 99.73% CPU
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+ Optimizing NNI: done in 0.000644582 secs
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+ Optimizing NNI: done in 0.000658519 secs using 70.16% CPU
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+ Optimizing NNI: done in 0.000650203 secs using 99.81% CPU
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+ Optimizing NNI: done in 0.000673918 secs using 99.86% CPU
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+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.00122079 secs using 99.94% CPU
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+ Optimizing NNI: done in 0.000625246 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000833606 secs using 99.93% CPU
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+ Optimizing NNI: done in 0.000204742 secs using 99.64% CPU
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+ Optimizing NNI: done in 0.000206194 secs using 99.42% CPU
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+ Iteration 30 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000249656 secs using 99.34% CPU
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+ Optimizing NNI: done in 0.000666033 secs using 99.84% CPU
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+ Optimizing NNI: done in 0.000633072 secs using 99.83% CPU
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+ Optimizing NNI: done in 0.000508219 secs
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+ Optimizing NNI: done in 0.000685609 secs using 45.8% CPU
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+ Optimizing NNI: done in 0.000708683 secs using 99.48% CPU
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+ Optimizing NNI: done in 0.000466461 secs using 99.9% CPU
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+ Optimizing NNI: done in 0.000424231 secs using 99.71% CPU
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+ Optimizing NNI: done in 0.000520872 secs using 99.64% CPU
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+ Optimizing NNI: done in 0.000988114 secs using 1.214% CPU
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+ Iteration 40 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000623232 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000663117 secs using 99.83% CPU
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+ Optimizing NNI: done in 0.00054122 secs using 99.77% CPU
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+ Optimizing NNI: done in 0.000631208 secs using 99.81% CPU
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+ Optimizing NNI: done in 0.00065394 secs using 99.86% CPU
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+ Optimizing NNI: done in 0.000645064 secs using 99.84% CPU
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+ Optimizing NNI: done in 0.000288789 secs using 98.34% CPU
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+ Optimizing NNI: done in 0.000603405 secs using 99.77% CPU
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+ Optimizing NNI: done in 0.000654271 secs
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+ Optimizing NNI: done in 0.000659972 secs using 81.82% CPU
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+ Iteration 50 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000421727 secs using 89.16% CPU
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+ Optimizing NNI: done in 0.000464126 secs using 99.76% CPU
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+ Optimizing NNI: done in 0.000668187 secs
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+ Optimizing NNI: done in 0.000209701 secs
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+ Optimizing NNI: done in 0.000208549 secs using 32.61% CPU
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+ Optimizing NNI: done in 0.000460509 secs using 99.89% CPU
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+ Optimizing NNI: done in 0.000645956 secs using 99.85% CPU
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+ Optimizing NNI: done in 0.000427648 secs using 99.85% CPU
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+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.000517596 secs using 99.69% CPU
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+ Optimizing NNI: done in 0.000511264 secs using 99.56% CPU
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+ Iteration 60 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000703683 secs using 98.91% CPU
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+ Optimizing NNI: done in 0.000458335 secs using 99.71% CPU
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+ Optimizing NNI: done in 0.000451051 secs using 99.77% CPU
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+ Optimizing NNI: done in 0.000454178 secs using 99.74% CPU
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+ Optimizing NNI: done in 0.000536741 secs using 99.86% CPU
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+ Optimizing NNI: done in 0.00043974 secs using 99.83% CPU
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+ Optimizing NNI: done in 0.000646577 secs using 99.76% CPU
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+ Optimizing NNI: done in 0.000493791 secs using 99.84% CPU
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+ Optimizing NNI: done in 0.000204842 secs using 99.59% CPU
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+ Optimizing NNI: done in 0.000464186 secs
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+ Iteration 70 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.00047201 secs
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+ Optimizing NNI: done in 0.00045498 secs using 98.47% CPU
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+ Optimizing NNI: done in 0.000373878 secs using 88.8% CPU
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+ Optimizing NNI: done in 0.000722138 secs using 99.84% CPU
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+ Optimizing NNI: done in 0.000205603 secs using 97.27% CPU
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+ Optimizing NNI: done in 0.00064866 secs using 99.9% CPU
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+ Optimizing NNI: done in 0.000501025 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000722497 secs using 99.79% CPU
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+ Optimizing NNI: done in 0.00043945 secs using 99.9% CPU
317
+ Optimizing NNI: done in 0.000196998 secs using 99.49% CPU
318
+ UPDATE BEST LOG-LIKELIHOOD: -674.481
319
+ Iteration 80 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
320
+ Optimizing NNI: done in 0.000201355 secs using 99.33% CPU
321
+ Optimizing NNI: done in 0.000454559 secs using 99.66% CPU
322
+ Optimizing NNI: done in 0.000518768 secs using 99.85% CPU
323
+ Optimizing NNI: done in 0.000204713 secs using 99.16% CPU
324
+ Optimizing NNI: done in 0.000481629 secs using 99.87% CPU
325
+ Optimizing NNI: done in 0.000195625 secs using 99.68% CPU
326
+ Optimizing NNI: done in 0.00043947 secs using 99.89% CPU
327
+ UPDATE BEST LOG-LIKELIHOOD: -674.481
328
+ Optimizing NNI: done in 0.000517165 secs using 99.77% CPU
329
+ Optimizing NNI: done in 0.00049828 secs using 99.74% CPU
330
+ Optimizing NNI: done in 0.000421847 secs using 99.8% CPU
331
+ Iteration 90 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
332
+ Optimizing NNI: done in 0.000205774 secs using 99.62% CPU
333
+ Optimizing NNI: done in 0.000674708 secs
334
+ Optimizing NNI: done in 0.000457274 secs
335
+ Optimizing NNI: done in 0.000385929 secs using 99.76% CPU
336
+ Optimizing NNI: done in 0.000474164 secs using 99.75% CPU
337
+ Optimizing NNI: done in 0.000494753 secs using 99.65% CPU
338
+ Optimizing NNI: done in 0.000419853 secs
339
+ Optimizing NNI: done in 0.000715395 secs using 35.92% CPU
340
+ Optimizing NNI: done in 0.000683946 secs using 99.57% CPU
341
+ Optimizing NNI: done in 0.000729591 secs using 99.92% CPU
342
+ Iteration 100 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
343
+ Optimizing NNI: done in 0.00022019 secs using 99.46% CPU
344
+ Optimizing NNI: done in 0.000455971 secs using 99.79% CPU
345
+ TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
346
+
347
+ --------------------------------------------------------------------
348
+ | FINALIZING TREE SEARCH |
349
+ --------------------------------------------------------------------
350
+ Performs final model parameters optimization
351
+ Estimate model parameters (epsilon = 0.010)
352
+ 1. Initial log-likelihood: -674.481
353
+ Optimal log-likelihood: -674.481
354
+ 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
355
+ Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
356
+ Parameters optimization took 1 rounds (0.000 sec)
357
+ BEST SCORE FOUND : -674.481
358
+ Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
359
+ Total tree length: 0.056
360
+
361
+ Total number of iterations: 102
362
+ CPU time used for tree search: 0.080 sec (0h:0m:0s)
363
+ Wall-clock time used for tree search: 0.082 sec (0h:0m:0s)
364
+ Total CPU time used: 0.154 sec (0h:0m:0s)
365
+ Total wall-clock time used: 0.169 sec (0h:0m:0s)
366
+
367
+ Analysis results written to:
368
+ IQ-TREE report: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree
369
+ Maximum-likelihood tree: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile
370
+ Likelihood distances: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist
371
+ Ancestral state: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
372
+ Screen log file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.log
373
+
374
+ Date and Time: Mon Aug 18 15:31:52 2025
test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist ADDED
@@ -0,0 +1,9 @@
1
+ 8
2
+ XnaiveX 0.0000000 0.0160006 0.0133100 0.0133100 0.0106285 0.0106285 0.0079575 0.0187007
3
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