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-0/out.treefile ADDED
@@ -0,0 +1 @@
1
+ (XnaiveX:0.0000010000,((18f4019708:0.0145918999,((308de1d739:0.0116507178,efdea248af:0.0087210277)Node5:0.0000010000,((5fb484a8a6:0.0145918997,(ee25049b92:0.0058202340,9c3cedb840:0.0028896479)Node8:0.0116795079)Node7:0.0000010000,(648902c3e5:0.0000010000,(8024ed1a22:0.0000010000,f47122f1f5:0.0000010000)Node10:0.0000010000)Node9:0.0058027364)Node6:0.0000010000)Node4:0.0000010000)Node3:0.0058027364,d024e5cab0:0.0000010000)Node2:0.0000010000,822801f8ab:0.0000010000)Node1;
test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa ADDED
@@ -0,0 +1,16 @@
1
+ >XnaiveX
2
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
3
+ >13de8675ec
4
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
5
+ >20a0129b57
6
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG
7
+ >31e052ee14
8
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
9
+ >33aaa62e12
10
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
11
+ >4233d708fe
12
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
13
+ >91796617a0
14
+ NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
15
+ >97366cf0d8
16
+ NNNCAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
test/ref-results/partition-new-simu/iqtree/iclust-1/log ADDED
@@ -0,0 +1,373 @@
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-1/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out -o XnaiveX
2
+ IQ-TREE version 3.0.1 for Linux x86 64-bit built May 5 2025
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+ Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
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+ 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-1/input-seqs.fa -pre /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out -o XnaiveX
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+ Seed: 784887 (Using SPRNG - Scalable Parallel Random Number Generator)
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+ Time: Mon Aug 18 15:31:52 2025
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+ Kernel: AVX+FMA - 1 threads (4 CPU cores detected)
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+
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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-1/input-seqs.fa ... Fasta format detected
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+ Reading fasta file: done in 7.5741e-05 secs
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+ Alignment most likely contains DNA/RNA sequences
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+ Constructing alignment: done in 0.000379799 secs
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+ WARNING: 3 sites contain only gaps or ambiguous characters.
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+ Alignment has 8 sequences with 370 columns, 7 distinct patterns
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+ 0 parsimony-informative, 2 singleton sites, 368 constant sites
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+ Gap/Ambiguity Composition p-value
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+ Analyzing sequences: done in 6.192e-06 secs
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+ 1 XnaiveX 0.81% passed 100.00%
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+ 2 13de8675ec 0.81% passed 100.00%
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+ 3 20a0129b57 0.81% passed 99.96%
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+ 4 31e052ee14 0.81% passed 100.00%
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+ 5 33aaa62e12 0.81% passed 100.00%
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+ 6 4233d708fe 0.81% passed 100.00%
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+ 7 91796617a0 0.81% passed 100.00%
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+ 8 97366cf0d8 0.81% passed 99.95%
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+ **** TOTAL 0.81% 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 0.000308676 secs using 59.61% CPU
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+ Estimate model parameters (epsilon = 1.000)
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+ 1. Initial log-likelihood: -519.628
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+ Optimal log-likelihood: -519.601
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+ Rate parameters: A-C: 0.00010 A-G: 3.78712 A-T: 0.00010 C-G: 0.00010 C-T: 0.00010 G-T: 1.00000
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+ Warning! Some parameters hit the boundaries
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+ Base frequencies: A: 0.237 C: 0.270 G: 0.294 T: 0.199
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+ Proportion of invariable sites: 0.497
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+ Gamma shape alpha: 998.448
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+ Parameters optimization took 1 rounds (0.001 sec)
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+ Time for fast ML tree search: 0.003 seconds
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+
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+ NOTE: ModelFinder requires 0 MB RAM!
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+ ModelFinder will test up to 968 DNA models (sample size: 370 epsilon: 0.100) ...
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+ No. Model -LnL df AIC AICc BIC
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+ 1 JC 524.779 13 1075.559 1076.581 1126.434
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+ 2 JC+I 524.779 14 1077.559 1078.742 1132.348
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+ 3 JC+G4 524.779 14 1077.559 1078.742 1132.348
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+ 4 JC+I+G4 524.782 15 1079.564 1080.920 1138.267
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+ 5 JC+R2 524.779 15 1079.559 1080.914 1138.261
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+ 6 JC+R3 524.779 17 1083.559 1085.297 1150.088
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+ 14 JC+I+R2 524.782 16 1081.564 1083.105 1144.180
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+ 15 JC+I+R3 524.782 18 1085.564 1087.513 1156.007
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+ 23 JC 524.779 13 1075.559 1076.581 1126.434
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+ 24 JC+I 524.779 14 1077.559 1078.742 1132.348
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+ 25 JC+G4 524.779 14 1077.559 1078.742 1132.348
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+ 45 F81 524.779 13 1075.559 1076.581 1126.434
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+ 46 F81+I 524.779 14 1077.559 1078.742 1132.348
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+ 47 F81+G4 524.779 14 1077.559 1078.742 1132.348
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+ 67 F81+F 521.218 16 1074.437 1075.978 1137.053
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+ 68 F81+F+I 521.218 17 1076.437 1078.175 1142.966
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+ 69 F81+F+G4 521.218 17 1076.437 1078.175 1142.966
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+ 89 K2P 524.663 14 1077.326 1078.509 1132.115
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+ 90 K2P+I 524.663 15 1079.326 1080.682 1138.028
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+ 91 K2P+G4 524.663 15 1079.326 1080.682 1138.028
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+ 111 K2P 524.663 14 1077.326 1078.509 1132.115
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+ 112 K2P+I 524.663 15 1079.326 1080.682 1138.028
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+ 113 K2P+G4 524.663 15 1079.326 1080.682 1138.028
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+ 133 HKY 524.663 14 1077.325 1078.508 1132.114
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+ 134 HKY+I 524.663 15 1079.325 1080.681 1138.028
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+ 135 HKY+G4 524.663 15 1079.325 1080.681 1138.028
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+ 155 HKY+F 521.099 17 1076.198 1077.937 1142.728
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+ 156 HKY+F+I 521.099 18 1078.198 1080.147 1148.641
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+ 157 HKY+F+G4 521.099 18 1078.198 1080.147 1148.641
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+ 177 TNe 524.028 15 1078.055 1079.411 1136.758
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+ 178 TNe+I 524.028 16 1080.055 1081.596 1142.671
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+ 179 TNe+G4 524.028 16 1080.055 1081.596 1142.671
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+ 199 TNe 524.028 15 1078.055 1079.411 1136.758
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+ 200 TNe+I 524.028 16 1080.055 1081.596 1142.671
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+ 201 TNe+G4 524.028 16 1080.055 1081.596 1142.671
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+ 221 TN 524.028 15 1078.055 1079.411 1136.758
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+ 222 TN+I 524.028 16 1080.055 1081.596 1142.671
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+ 223 TN+G4 524.028 16 1080.055 1081.596 1142.671
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+ 243 TN+F 520.525 18 1077.050 1078.999 1147.493
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+ 244 TN+F+I 520.525 19 1079.051 1081.222 1153.407
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+ 245 TN+F+G4 520.525 19 1079.050 1081.222 1153.407
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+ 265 K3P 523.995 15 1077.990 1079.346 1136.693
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+ 266 K3P+I 523.988 16 1079.976 1081.517 1142.592
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+ 267 K3P+G4 523.996 16 1079.991 1081.532 1142.607
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+ 287 K3P 523.995 15 1077.990 1079.346 1136.693
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+ 288 K3P+I 523.988 16 1079.976 1081.517 1142.592
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+ 289 K3P+G4 523.996 16 1079.991 1081.532 1142.607
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+ 309 K3Pu 523.971 15 1077.941 1079.297 1136.644
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+ 310 K3Pu+I 523.970 16 1079.940 1081.481 1142.556
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+ 311 K3Pu+G4 523.970 16 1079.940 1081.481 1142.556
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+ 331 K3Pu+F 520.390 18 1076.780 1078.729 1147.223
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+ 332 K3Pu+F+I 520.390 19 1078.780 1080.952 1153.137
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+ 333 K3Pu+F+G4 520.390 19 1078.780 1080.952 1153.137
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+ 353 TPM2 524.023 15 1078.046 1079.402 1136.749
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+ 354 TPM2+I 524.023 16 1080.046 1081.587 1142.662
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+ 355 TPM2+G4 524.023 16 1080.046 1081.588 1142.663
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+ 375 TPM2 524.023 15 1078.046 1079.402 1136.749
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+ 376 TPM2+I 524.023 16 1080.046 1081.587 1142.662
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+ 377 TPM2+G4 524.023 16 1080.046 1081.588 1142.663
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+ 397 TPM2u 524.023 15 1078.046 1079.402 1136.749
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+ 398 TPM2u+I 524.023 16 1080.046 1081.587 1142.662
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+ 399 TPM2u+G4 524.023 16 1080.046 1081.587 1142.662
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+ 419 TPM2u+F 520.505 18 1077.011 1078.959 1147.454
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+ 420 TPM2u+F+I 520.505 19 1079.010 1081.182 1153.367
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+ 421 TPM2u+F+G4 520.505 19 1079.010 1081.181 1153.367
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+ 441 TPM3 523.895 15 1077.791 1079.147 1136.493
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+ 442 TPM3+I 523.895 16 1079.791 1081.332 1142.407
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+ 443 TPM3+G4 523.895 16 1079.791 1081.332 1142.407
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+ 463 TPM3 523.895 15 1077.791 1079.147 1136.493
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+ 464 TPM3+I 523.895 16 1079.791 1081.332 1142.407
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+ 465 TPM3+G4 523.895 16 1079.791 1081.332 1142.407
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+ 485 TPM3u 523.895 15 1077.791 1079.147 1136.493
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+ 486 TPM3u+I 523.895 16 1079.791 1081.332 1142.407
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+ 487 TPM3u+G4 523.895 16 1079.791 1081.332 1142.407
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+ 507 TPM3u+F 520.242 18 1076.484 1078.433 1146.928
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+ 508 TPM3u+F+I 520.242 19 1078.484 1080.656 1152.841
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+ 509 TPM3u+F+G4 520.242 19 1078.484 1080.656 1152.841
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+ 529 TIMe 523.336 16 1078.671 1080.213 1141.288
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+ 530 TIMe+I 523.336 17 1080.671 1082.410 1147.201
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+ 531 TIMe+G4 523.336 17 1080.672 1082.410 1147.201
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+ 551 TIMe 523.336 16 1078.671 1080.213 1141.288
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+ 552 TIMe+I 523.336 17 1080.671 1082.410 1147.201
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+ 553 TIMe+G4 523.336 17 1080.672 1082.410 1147.201
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+ 573 TIM 523.336 16 1078.671 1080.213 1141.288
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+ 574 TIM+I 523.336 17 1080.671 1082.410 1147.201
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+ 575 TIM+G4 523.336 17 1080.672 1082.410 1147.201
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+ 595 TIM+F 519.818 19 1077.635 1079.806 1151.992
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+ 596 TIM+F+I 519.818 20 1079.636 1082.042 1157.906
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+ 597 TIM+F+G4 519.818 20 1079.635 1082.042 1157.905
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+ 617 TIM2e 523.390 16 1078.780 1080.321 1141.396
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+ 618 TIM2e+I 523.390 17 1080.780 1082.518 1147.309
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+ 619 TIM2e+G4 523.390 17 1080.780 1082.518 1147.309
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+ 639 TIM2e 523.390 16 1078.780 1080.321 1141.396
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+ 640 TIM2e+I 523.390 17 1080.780 1082.518 1147.309
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+ 641 TIM2e+G4 523.390 17 1080.780 1082.518 1147.309
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+ 661 TIM2 523.390 16 1078.780 1080.321 1141.396
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+ 662 TIM2+I 523.390 17 1080.780 1082.518 1147.309
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+ 663 TIM2+G4 523.390 17 1080.780 1082.518 1147.309
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+ 683 TIM2+F 519.933 19 1077.866 1080.037 1152.222
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+ 684 TIM2+F+I 519.933 20 1079.866 1082.273 1158.136
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+ 685 TIM2+F+G4 519.933 20 1079.866 1082.273 1158.136
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+ 705 TIM3e 523.262 16 1078.523 1080.064 1141.139
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+ 706 TIM3e+I 523.262 17 1080.523 1082.262 1147.053
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+ 707 TIM3e+G4 523.262 17 1080.523 1082.262 1147.053
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+ 727 TIM3e 523.262 16 1078.523 1080.064 1141.139
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+ 728 TIM3e+I 523.262 17 1080.523 1082.262 1147.053
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+ 729 TIM3e+G4 523.262 17 1080.523 1082.262 1147.053
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+ 749 TIM3 523.262 16 1078.523 1080.064 1141.139
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+ 750 TIM3+I 523.262 17 1080.523 1082.262 1147.053
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+ 751 TIM3+G4 523.262 17 1080.523 1082.262 1147.053
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+ 771 TIM3+F 519.670 19 1077.339 1079.511 1151.696
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+ 772 TIM3+F+I 519.669 20 1079.339 1081.746 1157.609
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+ 773 TIM3+F+G4 519.669 20 1079.339 1081.746 1157.609
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+ 793 TVMe 523.261 17 1080.522 1082.261 1147.052
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+ 794 TVMe+I 523.261 18 1082.522 1084.471 1152.965
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+ 795 TVMe+G4 523.261 18 1082.522 1084.471 1152.965
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+ 815 TVMe 523.261 17 1080.522 1082.261 1147.052
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+ 816 TVMe+I 523.261 18 1082.522 1084.471 1152.965
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+ 817 TVMe+G4 523.261 18 1082.522 1084.471 1152.965
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+ 837 TVM 523.261 17 1080.522 1082.261 1147.052
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+ 838 TVM+I 523.261 18 1082.522 1084.471 1152.965
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+ 839 TVM+G4 523.261 18 1082.522 1084.471 1152.965
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+ 859 TVM+F 519.650 20 1079.300 1081.707 1157.570
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+ 860 TVM+F+I 519.650 21 1081.300 1083.955 1163.483
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+ 861 TVM+F+G4 519.650 21 1081.300 1083.955 1163.483
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+ 881 SYM 522.627 18 1081.254 1083.203 1151.697
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+ 882 SYM+I 522.627 19 1083.254 1085.425 1157.611
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+ 883 SYM+G4 522.627 19 1083.254 1085.425 1157.611
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+ 903 SYM 522.627 18 1081.254 1083.203 1151.697
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+ 904 SYM+I 522.627 19 1083.254 1085.425 1157.611
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+ 905 SYM+G4 522.627 19 1083.254 1085.425 1157.611
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+ 925 GTR 522.627 18 1081.254 1083.203 1151.697
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+ 926 GTR+I 522.627 19 1083.254 1085.425 1157.611
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+ 927 GTR+G4 522.627 19 1083.254 1085.425 1157.611
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+ 947 GTR+F 519.077 21 1080.154 1082.810 1162.338
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+ 948 GTR+F+I 519.077 22 1082.154 1085.071 1168.251
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+ 949 GTR+F+G4 519.077 22 1082.154 1085.071 1168.251
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+ Akaike Information Criterion: F81+F
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+ Corrected Akaike Information Criterion: F81+F
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+ Bayesian Information Criterion: F81
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+ Best-fit model: F81 chosen according to BIC
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+
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+ All model information printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz
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+ CPU time for ModelFinder: 0.115 seconds (0h:0m:0s)
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+ Wall-clock time for ModelFinder: 0.130 seconds (0h:0m:0s)
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+
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+ NOTE: 0 MB RAM (0 GB) is required!
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+ Estimate model parameters (epsilon = 0.100)
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+ 1. Initial log-likelihood: -521.218
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+ Optimal log-likelihood: -521.218
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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: 0.237 C: 0.270 G: 0.294 T: 0.199
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+ Parameters optimization took 1 rounds (0.000 sec)
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+ Wrote distance file to...
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+ Computing ML distances based on estimated model parameters...
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+ Calculating distance matrix: done in 0.000120125 secs using 99.06% CPU
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+ Computing ML distances took 0.000137 sec (of wall-clock time) 0.000140 sec (of CPU time)
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+ Setting up auxiliary I and S matrices: done in 2.6339e-05 secs using 83.53% CPU
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+ Constructing RapidNJ tree: done in 4.2149e-05 secs using 85.41% CPU
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+ Computing RapidNJ tree took 0.000090 sec (of wall-clock time) 0.000078 sec (of CPU time)
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+ Log-likelihood of RapidNJ tree: -521.220
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+ --------------------------------------------------------------------
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+ | INITIALIZING CANDIDATE TREE SET |
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+ --------------------------------------------------------------------
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+ Generating 98 parsimony trees... 0.011 second
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+ Computing log-likelihood of 98 initial trees ... 0.011 seconds
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+ Current best score: -521.218
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+
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+ Do NNI search on 20 best initial trees
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+ Optimizing NNI: done in 0.000176579 secs using 87.78% CPU
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+ Estimate model parameters (epsilon = 0.100)
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+ BETTER TREE FOUND at iteration 1: -521.218
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+ Optimizing NNI: done in 0.000170098 secs using 87.6% CPU
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+ Optimizing NNI: done in 0.000167813 secs using 98.92% CPU
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+ Optimizing NNI: done in 0.000166631 secs using 99.02% CPU
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+ Optimizing NNI: done in 0.000167212 secs using 99.28% CPU
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+ Optimizing NNI: done in 0.000232724 secs using 99.26% CPU
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+ Optimizing NNI: done in 0.000207367 secs using 99.34% CPU
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+ Optimizing NNI: done in 0.000205183 secs using 99.42% CPU
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+ Optimizing NNI: done in 0.000206876 secs using 99.09% CPU
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+ Optimizing NNI: done in 0.000213028 secs using 99.52% CPU
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+ Iteration 10 / LogL: -521.218 / Time: 0h:0m:0s
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+ Optimizing NNI: done in 0.000216985 secs using 99.55% CPU
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+ Optimizing NNI: done in 0.000209201 secs using 99.43% CPU
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+ Optimizing NNI: done in 0.000229157 secs using 99.5% CPU
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+ Optimizing NNI: done in 0.000203209 secs using 99.41% CPU
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+ Optimizing NNI: done in 0.000207107 secs using 99.47% CPU
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+ Optimizing NNI: done in 0.000224719 secs using 99.68% CPU
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+ Optimizing NNI: done in 0.000207397 secs using 99.33% CPU
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+ Optimizing NNI: done in 0.000207266 secs using 99.87% CPU
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+ Optimizing NNI: done in 0.000211395 secs using 98.39% CPU
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+ Optimizing NNI: done in 0.000209511 secs using 99.76% CPU
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+ Iteration 20 / LogL: -521.218 / Time: 0h:0m:0s
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+ Finish initializing candidate tree set (20)
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+ Current best tree score: -521.218 / CPU time: 0.028
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+ Number of iterations: 20
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+ --------------------------------------------------------------------
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+ | OPTIMIZING CANDIDATE TREE SET |
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+ --------------------------------------------------------------------
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+ Optimizing NNI: done in 0.000168214 secs using 98.68% CPU
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+ Optimizing NNI: done in 0.000213499 secs using 99.3% CPU
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+ Optimizing NNI: done in 0.000159698 secs using 99.56% CPU
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+ Optimizing NNI: done in 0.000161611 secs using 94.05% CPU
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+ Optimizing NNI: done in 0.000206766 secs
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+ Optimizing NNI: done in 0.00019866 secs
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+ Optimizing NNI: done in 0.000157874 secs using 87.41% CPU
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+ Optimizing NNI: done in 0.000156201 secs using 87.71% CPU
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+ Optimizing NNI: done in 0.000161001 secs using 87.58% CPU
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+ Optimizing NNI: done in 0.000204602 secs using 99.22% CPU
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+ Iteration 30 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000162954 secs using 99.41% CPU
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+ Optimizing NNI: done in 0.00023065 secs using 99.72% CPU
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+ Optimizing NNI: done in 0.000158155 secs using 99.27% CPU
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+ Optimizing NNI: done in 0.000166801 secs using 99.52% CPU
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+ Optimizing NNI: done in 0.000201646 secs using 99.18% CPU
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+ Optimizing NNI: done in 0.000162884 secs using 98.84% CPU
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+ Optimizing NNI: done in 0.000215662 secs
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+ Optimizing NNI: done in 0.00016091 secs
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+ Optimizing NNI: done in 0.000159578 secs
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+ Optimizing NNI: done in 0.000205554 secs using 99.73% CPU
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+ Iteration 40 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000165779 secs using 94.7% CPU
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+ Optimizing NNI: done in 0.000173223 secs using 99.29% CPU
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+ Optimizing NNI: done in 0.000173473 secs using 99.15% CPU
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+ Optimizing NNI: done in 0.00019865 secs using 99.17% CPU
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+ Optimizing NNI: done in 0.00016043 secs using 99.11% CPU
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+ Optimizing NNI: done in 0.00016045 secs using 99.1% CPU
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+ Optimizing NNI: done in 0.000158255 secs using 90.36% CPU
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+ Optimizing NNI: done in 0.000158806 secs using 98.86% CPU
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+ Optimizing NNI: done in 0.000162052 secs using 99.35% CPU
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+ Optimizing NNI: done in 0.000224349 secs
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+ Iteration 50 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000158576 secs
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+ Optimizing NNI: done in 0.000208389 secs using 1.919% CPU
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+ Optimizing NNI: done in 0.000201456 secs using 99.28% CPU
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+ Optimizing NNI: done in 0.000172602 secs using 99.07% CPU
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+ Optimizing NNI: done in 0.000215653 secs using 99.23% CPU
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+ Optimizing NNI: done in 0.000202558 secs using 99.23% CPU
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+ Optimizing NNI: done in 0.000161871 secs using 99.46% CPU
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+ Optimizing NNI: done in 0.000160139 secs using 99.91% CPU
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+ Optimizing NNI: done in 0.000159538 secs using 99.04% CPU
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+ Optimizing NNI: done in 0.000195735 secs using 99.11% CPU
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+ Iteration 60 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000199342 secs using 99.33% CPU
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+ Optimizing NNI: done in 0.000159248 secs using 99.22% CPU
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+ Optimizing NNI: done in 0.000162874 secs using 98.85% CPU
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+ Optimizing NNI: done in 0.00016084 secs using 99.48% CPU
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+ Optimizing NNI: done in 0.000160851 secs using 95.12% CPU
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+ Optimizing NNI: done in 0.000220902 secs using 99.59% CPU
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+ Optimizing NNI: done in 0.000159017 secs using 99.36% CPU
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+ Optimizing NNI: done in 0.000216203 secs using 99.44% CPU
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+ Optimizing NNI: done in 0.000159418 secs using 99.11% CPU
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+ Optimizing NNI: done in 0.000161371 secs using 99.15% CPU
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+ Iteration 70 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000216534 secs using 99.29% CPU
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+ Optimizing NNI: done in 0.000156823 secs using 98.84% CPU
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+ Optimizing NNI: done in 0.000178843 secs using 99.53% CPU
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+ Optimizing NNI: done in 0.000159228 secs using 99.23% CPU
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+ Optimizing NNI: done in 0.000219189 secs using 99.46% CPU
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+ Optimizing NNI: done in 0.00020399 secs using 99.51% CPU
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+ Optimizing NNI: done in 0.000158136 secs using 99.28% CPU
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+ Optimizing NNI: done in 0.000184735 secs using 99.06% CPU
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+ Optimizing NNI: done in 0.00016096 secs using 99.4% CPU
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+ Optimizing NNI: done in 0.000201536 secs using 99.73% CPU
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+ Iteration 80 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000161391 secs using 99.14% CPU
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+ Optimizing NNI: done in 0.000204912 secs using 99.55% CPU
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+ Optimizing NNI: done in 0.000215503 secs using 98.84% CPU
323
+ Optimizing NNI: done in 0.000220651 secs using 99.25% CPU
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+ Optimizing NNI: done in 0.000157144 secs using 98.64% CPU
325
+ Optimizing NNI: done in 0.000200384 secs using 99.31% CPU
326
+ Optimizing NNI: done in 0.000157945 secs using 99.4% CPU
327
+ Optimizing NNI: done in 0.000183652 secs using 99.64% CPU
328
+ Optimizing NNI: done in 0.000158606 secs using 98.99% CPU
329
+ Optimizing NNI: done in 0.000159457 secs using 99.71% CPU
330
+ Iteration 90 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000205012 secs using 99.51% CPU
332
+ Optimizing NNI: done in 0.000208129 secs using 99.46% CPU
333
+ Optimizing NNI: done in 0.000157514 secs using 90.79% CPU
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+ Optimizing NNI: done in 0.000163976 secs
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+ Optimizing NNI: done in 0.000177841 secs
336
+ Optimizing NNI: done in 0.000174806 secs using 99.54% CPU
337
+ Optimizing NNI: done in 0.000206035 secs using 99.5% CPU
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+ Optimizing NNI: done in 0.000157975 secs using 99.38% CPU
339
+ Optimizing NNI: done in 0.000208429 secs using 99.31% CPU
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+ Optimizing NNI: done in 0.00019822 secs using 99.38% CPU
341
+ Iteration 100 / LogL: -521.218 / Time: 0h:0m:0s (0h:0m:0s left)
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+ Optimizing NNI: done in 0.000180217 secs using 98.77% CPU
343
+ Optimizing NNI: done in 0.000156411 secs using 99.1% CPU
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+ TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:0s
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+
346
+ --------------------------------------------------------------------
347
+ | FINALIZING TREE SEARCH |
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+ --------------------------------------------------------------------
349
+ Performs final model parameters optimization
350
+ Estimate model parameters (epsilon = 0.010)
351
+ 1. Initial log-likelihood: -521.218
352
+ Optimal log-likelihood: -521.218
353
+ 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
354
+ Base frequencies: A: 0.237 C: 0.270 G: 0.294 T: 0.199
355
+ Parameters optimization took 1 rounds (0.000 sec)
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+ BEST SCORE FOUND : -521.218
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+ Ancestral state probabilities printed to /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.state
358
+ Total tree length: 0.005
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+
360
+ Total number of iterations: 102
361
+ CPU time used for tree search: 0.063 sec (0h:0m:0s)
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+ Wall-clock time used for tree search: 0.060 sec (0h:0m:0s)
363
+ Total CPU time used: 0.191 sec (0h:0m:0s)
364
+ Total wall-clock time used: 0.205 sec (0h:0m:0s)
365
+
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+ Analysis results written to:
367
+ IQ-TREE report: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree
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+ Maximum-likelihood tree: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile
369
+ Likelihood distances: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.mldist
370
+ Ancestral state: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.state
371
+ Screen log file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/iqtree/iclust-1/out.log
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+
373
+ Date and Time: Mon Aug 18 15:31:52 2025
test/ref-results/partition-new-simu/iqtree/iclust-1/out.bionj ADDED
@@ -0,0 +1 @@
1
+ ((XnaiveX:-1.1408702e-08,20a0129b57:0.0027295852):1.2788223e-06,((13de8675ec:5e-07,4233d708fe:5e-07):0,(31e052ee14:5e-07,33aaa62e12:5e-07):0):-1.2788184e-06,(91796617a0:-3.5273843e-07,97366cf0d8:0.0027299265):1.2788223e-06);