partis-bcr 1.0.8__py3-none-any.whl → 1.0.8.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-1.0.8.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.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 +5 -5
  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 +8 -8
  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 +85 -101
  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 +394 -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 +393 -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 +414 -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 +413 -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 +376 -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 +375 -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 +453 -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-1.0.8.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  145. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  146. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  147. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  148. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/gctree-run.py +0 -0
  149. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  150. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/parse-output.py +0 -0
  151. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/partis-test.py +0 -0
  152. {partis_bcr-1.0.8.data → partis_bcr-1.0.8.post1.dev1.data}/scripts/split-loci.py +0 -0
  153. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/WHEEL +0 -0
  154. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/entry_points.txt +0 -0
  155. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/licenses/COPYING +0 -0
  156. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.8.post1.dev1.dist-info}/top_level.txt +0 -0
test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile ADDED
@@ -0,0 +1 @@
1
+ (XnaiveX:0.0000010000,13de8675ec:0.0000010000,(((20a0129b57:0.0027295720,97366cf0d8:0.0027295728)Node4:0.0000010000,4233d708fe:0.0000010000)Node3:0.0000010000,(31e052ee14:0.0000010000,(33aaa62e12:0.0000010000,91796617a0:0.0000010000)Node6:0.0000010000)Node5:0.0000010000)Node2:0.0000010000)Node1;
test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa ADDED
@@ -0,0 +1,16 @@
1
+ >XnaiveX
2
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
3
+ >162cb1691f
4
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG
5
+ >17f57acf2e
6
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
7
+ >73431a9b10
8
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
9
+ >73d6c6e558
10
+ CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
11
+ >948b83fb4d
12
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
13
+ >bf50fa2017
14
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
15
+ >c8a90cc3d7
16
+ CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
test/ref-results/partition-new-simu/iqtree/iclust-2/log ADDED
@@ -0,0 +1,376 @@
1
+ run /home/runner/work/partis/partis/bin/iqtree-3-linux -asr -s /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out -o XnaiveX
2
+ IQ-TREE version 3.0.1 for Linux x86 64-bit built May 5 2025
3
+ Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
4
+ Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow,
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+ Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt
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+
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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-2/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out -o XnaiveX
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+ Seed: 617209 (Using SPRNG - Scalable Parallel Random Number Generator)
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+ Time: Sat Aug 16 23:08:16 2025
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+ Kernel: AVX+FMA - 1 threads (4 CPU cores detected)
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+
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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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+
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+ Reading alignment file /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa ... Fasta format detected
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+ Reading fasta file: done in 0.000877834 secs
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+ Alignment most likely contains DNA/RNA sequences
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+ Constructing alignment: done in 0.000427405 secs using 25.03% CPU
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+ Alignment has 8 sequences with 379 columns, 21 distinct patterns
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+ 4 parsimony-informative, 17 singleton sites, 358 constant sites
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+ Gap/Ambiguity Composition p-value
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+ Analyzing sequences: done in 8.636e-06 secs using 92.64% CPU
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+ 1 XnaiveX 0.00% passed 99.90%
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+ 2 162cb1691f 0.00% passed 99.94%
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+ 3 17f57acf2e 0.00% passed 99.94%
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+ 4 73431a9b10 0.00% passed 99.81%
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+ 5 73d6c6e558 0.00% passed 98.68%
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+ 6 948b83fb4d 0.00% passed 99.88%
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+ 7 bf50fa2017 0.00% passed 99.81%
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+ 8 c8a90cc3d7 0.00% passed 99.56%
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+ **** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=3)
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+
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+
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+ Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
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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 0.000489232 secs using 66.84% CPU
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+ Estimate model parameters (epsilon = 1.000)
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+ 1. Initial log-likelihood: -668.906
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+ Optimal log-likelihood: -668.900
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+ Rate parameters: A-C: 0.58043 A-G: 0.19277 A-T: 0.25950 C-G: 0.74204 C-T: 1.19038 G-T: 1.00000
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+ Base frequencies: A: 0.219 C: 0.280 G: 0.285 T: 0.216
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+ Proportion of invariable sites: 0.470
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+ Gamma shape alpha: 998.448
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+ Parameters optimization took 1 rounds (0.002 sec)
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+ Time for fast ML tree search: 0.004 seconds
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+
50
+ NOTE: ModelFinder requires 0 MB RAM!
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+ ModelFinder will test up to 968 DNA models (sample size: 379 epsilon: 0.100) ...
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+ No. Model -LnL df AIC AICc BIC
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+ 1 JC 674.481 13 1374.962 1375.959 1426.150
54
+ 2 JC+I 674.481 14 1376.962 1378.116 1432.088
55
+ 3 JC+G4 674.481 14 1376.963 1378.117 1432.088
56
+ 4 JC+I+G4 674.940 15 1379.879 1381.201 1438.942
57
+ 5 JC+R2 674.481 15 1378.963 1380.285 1438.026
58
+ 6 JC+R3 674.481 17 1382.962 1384.658 1449.900
59
+ 14 JC+I+R2 674.942 16 1381.884 1383.387 1444.884
60
+ 15 JC+I+R3 674.935 18 1385.870 1387.770 1456.746
61
+ 23 JC 674.481 13 1374.962 1375.959 1426.150
62
+ 24 JC+I 674.481 14 1376.962 1378.116 1432.088
63
+ 25 JC+G4 674.481 14 1376.963 1378.117 1432.088
64
+ 45 F81 674.481 13 1374.962 1375.959 1426.150
65
+ 46 F81+I 674.481 14 1376.962 1378.116 1432.088
66
+ 47 F81+G4 674.481 14 1376.963 1378.117 1432.088
67
+ 67 F81+F 671.490 16 1374.980 1376.482 1437.980
68
+ 68 F81+F+I 671.490 17 1376.980 1378.675 1443.918
69
+ 69 F81+F+G4 671.490 17 1376.980 1378.676 1443.918
70
+ 89 K2P 674.481 14 1376.962 1378.116 1432.087
71
+ 90 K2P+I 674.481 15 1378.962 1380.284 1438.025
72
+ 91 K2P+G4 674.481 15 1378.963 1380.285 1438.026
73
+ 111 K2P 674.481 14 1376.962 1378.116 1432.087
74
+ 112 K2P+I 674.481 15 1378.962 1380.284 1438.025
75
+ 113 K2P+G4 674.481 15 1378.963 1380.285 1438.026
76
+ 133 HKY 674.481 14 1376.962 1378.116 1432.087
77
+ 134 HKY+I 674.481 15 1378.962 1380.284 1438.025
78
+ 135 HKY+G4 674.481 15 1378.963 1380.285 1438.026
79
+ 155 HKY+F 671.489 17 1376.977 1378.673 1443.916
80
+ 156 HKY+F+I 671.489 18 1378.977 1380.877 1449.853
81
+ 157 HKY+F+G4 671.489 18 1378.978 1380.878 1449.854
82
+ 177 TNe 672.458 15 1374.916 1376.238 1433.979
83
+ 178 TNe+I 672.458 16 1376.916 1378.419 1439.917
84
+ 179 TNe+G4 672.458 16 1376.917 1378.420 1439.917
85
+ 199 TNe 672.458 15 1374.916 1376.238 1433.979
86
+ 200 TNe+I 672.458 16 1376.916 1378.419 1439.917
87
+ 201 TNe+G4 672.458 16 1376.917 1378.420 1439.917
88
+ 221 TN 672.458 15 1374.916 1376.238 1433.979
89
+ 222 TN+I 672.458 16 1376.916 1378.419 1439.917
90
+ 223 TN+G4 672.458 16 1376.917 1378.420 1439.917
91
+ 243 TN+F 669.425 18 1374.851 1376.751 1445.726
92
+ 244 TN+F+I 669.425 19 1376.851 1378.968 1451.664
93
+ 245 TN+F+G4 669.426 19 1376.852 1378.969 1451.665
94
+ 265 K3P 674.338 15 1378.676 1379.998 1437.739
95
+ 266 K3P+I 674.338 16 1380.676 1382.179 1443.676
96
+ 267 K3P+G4 674.338 16 1380.677 1382.179 1443.677
97
+ 287 K3P 674.338 15 1378.676 1379.998 1437.739
98
+ 288 K3P+I 674.338 16 1380.676 1382.179 1443.676
99
+ 289 K3P+G4 674.338 16 1380.677 1382.179 1443.677
100
+ 309 K3Pu 674.338 15 1378.676 1379.998 1437.739
101
+ 310 K3Pu+I 674.338 16 1380.676 1382.179 1443.676
102
+ 311 K3Pu+G4 674.338 16 1380.677 1382.179 1443.677
103
+ 331 K3Pu+F 671.310 18 1378.621 1380.521 1449.496
104
+ 332 K3Pu+F+I 671.310 19 1380.620 1382.737 1455.433
105
+ 333 K3Pu+F+G4 671.311 19 1380.621 1382.738 1455.434
106
+ 353 TPM2 673.519 15 1377.038 1378.360 1436.101
107
+ 354 TPM2+I 673.519 16 1379.038 1380.541 1442.039
108
+ 355 TPM2+G4 673.519 16 1379.039 1380.542 1442.039
109
+ 375 TPM2 673.519 15 1377.038 1378.360 1436.101
110
+ 376 TPM2+I 673.519 16 1379.038 1380.541 1442.039
111
+ 377 TPM2+G4 673.519 16 1379.039 1380.542 1442.039
112
+ 397 TPM2u 673.519 15 1377.038 1378.360 1436.101
113
+ 398 TPM2u+I 673.519 16 1379.038 1380.541 1442.038
114
+ 399 TPM2u+G4 673.519 16 1379.039 1380.542 1442.039
115
+ 419 TPM2u+F 670.831 18 1377.663 1379.563 1448.539
116
+ 420 TPM2u+F+I 670.831 19 1379.663 1381.780 1454.476
117
+ 421 TPM2u+F+G4 670.832 19 1379.664 1381.781 1454.477
118
+ 441 TPM3 674.438 15 1378.877 1380.199 1437.940
119
+ 442 TPM3+I 674.438 16 1380.877 1382.379 1443.877
120
+ 443 TPM3+G4 674.439 16 1380.877 1382.380 1443.878
121
+ 463 TPM3 674.438 15 1378.877 1380.199 1437.940
122
+ 464 TPM3+I 674.438 16 1380.877 1382.379 1443.877
123
+ 465 TPM3+G4 674.439 16 1380.877 1382.380 1443.878
124
+ 485 TPM3u 674.438 15 1378.876 1380.199 1437.940
125
+ 486 TPM3u+I 674.438 16 1380.876 1382.379 1443.877
126
+ 487 TPM3u+G4 674.439 16 1380.877 1382.380 1443.878
127
+ 507 TPM3u+F 671.487 18 1378.975 1380.875 1449.851
128
+ 508 TPM3u+F+I 671.487 19 1380.975 1383.092 1455.788
129
+ 509 TPM3u+F+G4 671.488 19 1380.975 1383.092 1455.789
130
+ 529 TIMe 672.315 16 1376.630 1378.133 1439.630
131
+ 530 TIMe+I 672.315 17 1378.630 1380.325 1445.568
132
+ 531 TIMe+G4 672.315 17 1378.631 1380.326 1445.569
133
+ 551 TIMe 672.315 16 1376.630 1378.133 1439.630
134
+ 552 TIMe+I 672.315 17 1378.630 1380.325 1445.568
135
+ 553 TIMe+G4 672.315 17 1378.631 1380.326 1445.569
136
+ 573 TIM 672.315 16 1376.630 1378.133 1439.630
137
+ 574 TIM+I 672.315 17 1378.630 1380.325 1445.568
138
+ 575 TIM+G4 672.315 17 1378.631 1380.326 1445.569
139
+ 595 TIM+F 669.247 19 1376.494 1378.611 1451.307
140
+ 596 TIM+F+I 669.247 20 1378.494 1380.840 1457.245
141
+ 597 TIM+F+G4 669.247 20 1378.495 1380.841 1457.246
142
+ 617 TIM2e 671.494 16 1374.988 1376.491 1437.988
143
+ 618 TIM2e+I 671.494 17 1376.988 1378.683 1443.926
144
+ 619 TIM2e+G4 671.494 17 1376.989 1378.684 1443.927
145
+ 639 TIM2e 671.494 16 1374.988 1376.491 1437.988
146
+ 640 TIM2e+I 671.494 17 1376.988 1378.683 1443.926
147
+ 641 TIM2e+G4 671.494 17 1376.989 1378.684 1443.927
148
+ 661 TIM2 671.494 16 1374.988 1376.491 1437.988
149
+ 662 TIM2+I 671.494 17 1376.988 1378.683 1443.926
150
+ 663 TIM2+G4 671.494 17 1376.989 1378.684 1443.927
151
+ 683 TIM2+F 668.767 19 1375.534 1377.651 1450.348
152
+ 684 TIM2+F+I 668.767 20 1377.534 1379.881 1456.285
153
+ 685 TIM2+F+G4 668.768 20 1377.535 1379.882 1456.286
154
+ 705 TIM3e 672.415 16 1376.831 1378.333 1439.831
155
+ 706 TIM3e+I 672.415 17 1378.831 1380.526 1445.769
156
+ 707 TIM3e+G4 672.416 17 1378.832 1380.527 1445.770
157
+ 727 TIM3e 672.415 16 1376.831 1378.333 1439.831
158
+ 728 TIM3e+I 672.415 17 1378.831 1380.526 1445.769
159
+ 729 TIM3e+G4 672.416 17 1378.832 1380.527 1445.770
160
+ 749 TIM3 672.415 16 1376.831 1378.333 1439.831
161
+ 750 TIM3+I 672.415 17 1378.831 1380.526 1445.769
162
+ 751 TIM3+G4 672.416 17 1378.832 1380.527 1445.770
163
+ 771 TIM3+F 669.424 19 1376.849 1378.966 1451.662
164
+ 772 TIM3+F+I 669.424 20 1378.849 1381.195 1457.599
165
+ 773 TIM3+F+G4 669.425 20 1378.850 1381.196 1457.600
166
+ 793 TVMe 673.109 17 1380.218 1381.914 1447.157
167
+ 794 TVMe+I 673.109 18 1382.218 1384.118 1453.094
168
+ 795 TVMe+G4 673.110 18 1382.219 1384.119 1453.095
169
+ 815 TVMe 673.109 17 1380.218 1381.914 1447.157
170
+ 816 TVMe+I 673.109 18 1382.218 1384.118 1453.094
171
+ 817 TVMe+G4 673.110 18 1382.219 1384.119 1453.095
172
+ 837 TVM 673.109 17 1380.218 1381.914 1447.156
173
+ 838 TVM+I 673.109 18 1382.218 1384.118 1453.094
174
+ 839 TVM+G4 673.109 18 1382.219 1384.119 1453.095
175
+ 859 TVM+F 670.452 20 1380.904 1383.251 1459.655
176
+ 860 TVM+F+I 670.452 21 1382.904 1385.493 1465.593
177
+ 861 TVM+F+G4 670.453 21 1382.905 1385.493 1465.593
178
+ 881 SYM 671.084 18 1378.168 1380.068 1449.043
179
+ 882 SYM+I 671.084 19 1380.168 1382.285 1454.981
180
+ 883 SYM+G4 671.084 19 1380.169 1382.286 1454.982
181
+ 903 SYM 671.084 18 1378.168 1380.068 1449.043
182
+ 904 SYM+I 671.084 19 1380.168 1382.285 1454.981
183
+ 905 SYM+G4 671.084 19 1380.169 1382.286 1454.982
184
+ 925 GTR 671.084 18 1378.168 1380.068 1449.043
185
+ 926 GTR+I 671.084 19 1380.168 1382.285 1454.981
186
+ 927 GTR+G4 671.084 19 1380.169 1382.286 1454.982
187
+ 947 GTR+F 668.388 21 1378.775 1381.363 1461.463
188
+ 948 GTR+F+I 668.388 22 1380.775 1383.618 1467.401
189
+ 949 GTR+F+G4 668.388 22 1380.776 1383.619 1467.402
190
+ Akaike Information Criterion: TN+F
191
+ Corrected Akaike Information Criterion: JC
192
+ Bayesian Information Criterion: JC
193
+ Best-fit model: JC chosen according to BIC
194
+
195
+ All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz
196
+ CPU time for ModelFinder: 0.105 seconds (0h:0m:0s)
197
+ Wall-clock time for ModelFinder: 0.108 seconds (0h:0m:0s)
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+
199
+ NOTE: 0 MB RAM (0 GB) is required!
200
+ Estimate model parameters (epsilon = 0.100)
201
+ 1. Initial log-likelihood: -674.481
202
+ Optimal log-likelihood: -674.481
203
+ 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
204
+ Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
205
+ Parameters optimization took 1 rounds (0.000 sec)
206
+ Wrote distance file to...
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+ Computing ML distances based on estimated model parameters...
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+ Calculating distance matrix: done in 0.000171813 secs using 99.53% CPU
209
+ Computing ML distances took 0.000190 sec (of wall-clock time) 0.000193 sec (of CPU time)
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+ Setting up auxiliary I and S matrices: done in 2.6009e-05 secs using 92.28% CPU
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+ Constructing RapidNJ tree: done in 3.2872e-05 secs using 91.26% CPU
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+ Computing RapidNJ tree took 0.000080 sec (of wall-clock time) 0.000076 sec (of CPU time)
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+ Log-likelihood of RapidNJ tree: -680.247
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+ --------------------------------------------------------------------
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+ | INITIALIZING CANDIDATE TREE SET |
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+ --------------------------------------------------------------------
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+ Generating 98 parsimony trees... 0.021 second
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+ Computing log-likelihood of 72 initial trees ... 0.009 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 0.000353666 secs using 99.53% CPU
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+ Estimate model parameters (epsilon = 0.100)
224
+ BETTER TREE FOUND at iteration 1: -674.481
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+ Optimizing NNI: done in 0.000267734 secs using 99.35% CPU
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+ Optimizing NNI: done in 0.000343177 secs using 99.37% CPU
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+ Optimizing NNI: done in 0.000320664 secs using 99.48% CPU
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+ Optimizing NNI: done in 0.000338298 secs using 99.62% CPU
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+ Optimizing NNI: done in 0.000331074 secs using 99.68% CPU
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+ Optimizing NNI: done in 0.000309172 secs using 99.62% CPU
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+ Optimizing NNI: done in 0.000346473 secs using 99.57% CPU
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+ Optimizing NNI: done in 0.000333158 secs using 99.65% CPU
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+ Optimizing NNI: done in 0.00070038 secs using 99.8% CPU
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+ Iteration 10 / LogL: -674.481 / Time: 0h:0m:0s
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+ Optimizing NNI: done in 0.000697384 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000297149 secs using 99.61% CPU
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+ Optimizing NNI: done in 0.000684049 secs using 99.85% CPU
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+ Optimizing NNI: done in 0.000706851 secs using 99.88% CPU
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+ Optimizing NNI: done in 0.000688758 secs using 99.74% CPU
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+ Optimizing NNI: done in 0.000666826 secs using 99.88% CPU
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+ Optimizing NNI: done in 0.00032399 secs using 99.69% CPU
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+ Optimizing NNI: done in 0.000901418 secs using 99.84% CPU
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+ Optimizing NNI: done in 0.000308531 secs using 99.5% CPU
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+ Optimizing NNI: done in 0.000606072 secs using 99.66% CPU
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+ Iteration 20 / LogL: -674.482 / Time: 0h:0m:0s
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+ Finish initializing candidate tree set (7)
247
+ Current best tree score: -674.481 / CPU time: 0.042
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+ Number of iterations: 20
249
+ --------------------------------------------------------------------
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+ | OPTIMIZING CANDIDATE TREE SET |
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+ --------------------------------------------------------------------
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+ Optimizing NNI: done in 0.000697163 secs using 99.69% CPU
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+ Optimizing NNI: done in 0.000681163 secs using 98.51% CPU
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+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.0006056 secs
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+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.000208623 secs
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+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.000528726 secs using 84.54% CPU
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+ Optimizing NNI: done in 0.000453484 secs using 93.72% CPU
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+ Optimizing NNI: done in 0.00043496 secs
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+ Optimizing NNI: done in 0.000415462 secs using 15.16% CPU
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+ Optimizing NNI: done in 0.000422236 secs using 99.71% CPU
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+ Optimizing NNI: done in 0.000670524 secs
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+ Iteration 30 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000465767 secs using 0.6441% CPU
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+ Optimizing NNI: done in 0.000492578 secs
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+ Optimizing NNI: done in 0.000460006 secs
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+ Optimizing NNI: done in 0.000169329 secs
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+ Optimizing NNI: done in 0.000384344 secs
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+ Optimizing NNI: done in 0.000184748 secs using 89.85% CPU
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+ Optimizing NNI: done in 0.000423297 secs using 91.43% CPU
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+ Optimizing NNI: done in 0.000498488 secs
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+ Optimizing NNI: done in 0.000436763 secs
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+ Optimizing NNI: done in 0.000451471 secs
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+ Iteration 40 / LogL: -680.246 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000448715 secs
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+ Optimizing NNI: done in 0.000414591 secs using 99.86% CPU
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+ Optimizing NNI: done in 0.000444667 secs using 98.05% CPU
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+ Optimizing NNI: done in 0.000416995 secs using 99.76% CPU
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+ Optimizing NNI: done in 0.000489281 secs using 99.74% CPU
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+ Optimizing NNI: done in 0.000629957 secs using 99.85% CPU
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+ Optimizing NNI: done in 0.000478532 secs using 99.89% CPU
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+ Optimizing NNI: done in 0.000695891 secs using 99.15% CPU
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+ Optimizing NNI: done in 0.000615019 secs using 99.83% CPU
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+ Optimizing NNI: done in 0.000458724 secs using 99.84% 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 0.000480496 secs using 99.69% CPU
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+ Optimizing NNI: done in 0.000480025 secs using 99.79% CPU
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+ Optimizing NNI: done in 0.000470066 secs using 99.77% CPU
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+ Optimizing NNI: done in 0.000434528 secs using 99.88% CPU
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+ Optimizing NNI: done in 0.000486737 secs
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+ Optimizing NNI: done in 0.000423918 secs using 5.426% CPU
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+ Optimizing NNI: done in 0.000419811 secs using 99.81% CPU
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+ Optimizing NNI: done in 0.000387069 secs using 99.21% CPU
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+ Optimizing NNI: done in 0.000581656 secs using 99.72% CPU
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+ Optimizing NNI: done in 0.000437735 secs using 98.92% CPU
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+ Iteration 60 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000426413 secs using 99.67% CPU
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+ Optimizing NNI: done in 0.000671686 secs
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+ Optimizing NNI: done in 0.000690701 secs
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+ Optimizing NNI: done in 0.000205397 secs
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+ Optimizing NNI: done in 0.000484994 secs using 83.09% CPU
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+ Optimizing NNI: done in 0.000719526 secs using 92.98% CPU
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+ Optimizing NNI: done in 0.000425782 secs using 99.82% CPU
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+ Optimizing NNI: done in 0.000510622 secs using 96.74% CPU
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+ Optimizing NNI: done in 0.000726909 secs using 99.87% CPU
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+ Optimizing NNI: done in 0.000933598 secs using 99.94% CPU
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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 0.000464304 secs using 99.72% CPU
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+ Optimizing NNI: done in 0.000424309 secs using 99.93% CPU
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+ Optimizing NNI: done in 0.000480495 secs using 99.69% CPU
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+ Optimizing NNI: done in 0.000672577 secs using 99.91% CPU
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+ Optimizing NNI: done in 0.000682015 secs using 99.85% CPU
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+ Optimizing NNI: done in 0.000653111 secs using 99.83% CPU
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+ Optimizing NNI: done in 0.000401807 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000668379 secs using 99.94% CPU
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+ Optimizing NNI: done in 0.000454627 secs using 99.64% CPU
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+ Optimizing NNI: done in 0.000450088 secs using 99.76% CPU
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+ Iteration 80 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.00020158 secs using 99.22% CPU
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+ Optimizing NNI: done in 0.000415042 secs using 99.75% CPU
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+ Optimizing NNI: done in 0.000427195 secs using 99.72% CPU
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+ Optimizing NNI: done in 0.000582096 secs using 99.81% CPU
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+ Optimizing NNI: done in 0.000463854 secs using 99.82% CPU
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+ Optimizing NNI: done in 0.000469805 secs using 99.83% CPU
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+ Optimizing NNI: done in 0.000657859 secs using 99.87% CPU
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+ Optimizing NNI: done in 0.000657339 secs using 99.8% CPU
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+ Optimizing NNI: done in 0.000474103 secs using 99.77% CPU
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+ Optimizing NNI: done in 0.000673439 secs using 99.93% CPU
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+ Iteration 90 / LogL: -674.482 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000193876 secs using 99.55% CPU
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+ Optimizing NNI: done in 0.000205647 secs using 99.2% CPU
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+ Optimizing NNI: done in 0.000439999 secs using 99.77% CPU
335
+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.000688607 secs using 99.91% CPU
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+ Optimizing NNI: done in 0.000462341 secs using 99.71% CPU
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+ Optimizing NNI: done in 0.000466289 secs
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+ Optimizing NNI: done in 0.000434639 secs
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+ UPDATE BEST LOG-LIKELIHOOD: -674.481
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+ Optimizing NNI: done in 0.000492878 secs using 99.82% CPU
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+ Optimizing NNI: done in 0.000201219 secs using 99.39% CPU
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+ Optimizing NNI: done in 0.000403871 secs using 94.34% CPU
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+ Iteration 100 / LogL: -674.481 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000428498 secs using 99.88% CPU
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+ Optimizing NNI: done in 0.000653541 secs using 99.76% CPU
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+ TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
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+
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+ --------------------------------------------------------------------
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+ | FINALIZING TREE SEARCH |
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+ --------------------------------------------------------------------
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+ Performs final model parameters optimization
353
+ Estimate model parameters (epsilon = 0.010)
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+ 1. Initial log-likelihood: -674.481
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+ Optimal log-likelihood: -674.481
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+ 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
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+ Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
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+ Parameters optimization took 1 rounds (0.000 sec)
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+ BEST SCORE FOUND : -674.481
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+ Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
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+ Total tree length: 0.056
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+
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+ Total number of iterations: 102
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+ CPU time used for tree search: 0.087 sec (0h:0m:0s)
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+ Wall-clock time used for tree search: 0.092 sec (0h:0m:0s)
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+ Total CPU time used: 0.204 sec (0h:0m:0s)
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+ Total wall-clock time used: 0.215 sec (0h:0m:0s)
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+
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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-2/out.iqtree
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+ Maximum-likelihood tree: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile
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+ Likelihood distances: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist
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+ Ancestral state: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.state
374
+ Screen log file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-2/out.log
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+
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+ Date and Time: Sat Aug 16 23:08:16 2025
test/ref-results/partition-new-simu/iqtree/iclust-2/out.bionj ADDED
@@ -0,0 +1 @@
1
+ ((XnaiveX:0.0025902023,c8a90cc3d7:0.016110541):0.001381147,((162cb1691f:0.0053297933,17f57acf2e:0.002627736):0.0047392142,73d6c6e558:0.011337848):-0.0013482573,(948b83fb4d:0.0061970716,(73431a9b10:0.0053405152,bf50fa2017:-4.4832937e-05):0.001788862):0.0013337678);