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

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Files changed (95) hide show
  1. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +95 -95
  3. test/new-results/get-selection-metrics-new-simu.yaml +1 -1
  4. test/new-results/test.log +2 -2
  5. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  8. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +3 -3
  9. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +1 -1
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  25. test/paired/new-results/run-times.csv +6 -6
  26. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -6
  27. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
  28. test/paired/new-results/subset-partition-new-simu/merged-partition.log +3 -3
  29. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  32. test/paired/new-results/test.log +33 -33
  33. test/ref-results/partition-new-simu/iqtree/iclust-0/log +187 -151
  34. test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
  35. test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +34 -34
  36. test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +187 -151
  37. test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
  38. test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +2820 -2820
  39. test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -1
  40. test/ref-results/partition-new-simu/iqtree/iclust-1/log +166 -207
  41. test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
  42. test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +151 -151
  43. test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +166 -207
  44. test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
  45. test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +740 -740
  46. test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -1
  47. test/ref-results/partition-new-simu/iqtree/iclust-2/log +134 -135
  48. test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
  49. test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +17 -17
  50. test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +134 -135
  51. test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
  52. test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +763 -763
  53. test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -1
  54. test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -1
  55. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +30 -30
  56. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +7 -7
  57. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -1
  58. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -1
  59. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -1
  60. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  61. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +87 -87
  62. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -20
  63. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -20
  64. test/ref-results/partition-new-simu/raxml/iclust-0/log +198 -197
  65. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -1
  66. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -1
  67. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  68. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +54 -54
  69. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -20
  70. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -20
  71. test/ref-results/partition-new-simu/raxml/iclust-1/log +112 -112
  72. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +22 -22
  73. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -6
  74. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -1
  75. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -1
  76. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -1
  77. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -1
  78. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +84 -84
  79. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -20
  80. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -20
  81. test/ref-results/partition-new-simu/raxml/iclust-2/log +182 -182
  82. test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -1
  83. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  84. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  85. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  86. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  87. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
  88. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  89. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
  90. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
  91. {partis_bcr-1.0.8.post1.dev1.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
  92. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
  93. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
  94. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
  95. {partis_bcr-1.0.8.post1.dev1.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml CHANGED
@@ -1 +1 @@
1
- {"version-info": {"partis-yaml": 0.1, "partis-git": {"commit": "3d759975d125203c297c47325f43244d8de1bfda", "tag": "v1.0.8", "n_ahead_of_tag": "1"}}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ4*01": "TTTTGTATTTGGTGGAGGAACCCAGCTGATCATTTTAG", "IGLJ5*01": "CTGGGTGTTTGGTGAGGGGACCGAGCTGACCGTCCTAG", "IGLJ5*02": "CTGGGTGTTTGGTGAGGGGACGGAGCTGACCGTCCTAG", "IGLJ6*01": "TAATGTGTTCGGCAGTGGCACCAAGGTGACCGTCCTCG", "IGLJ7*01": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGTCCTCG", "IGLJ7*02": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGCCCTCG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ5*02": 7, "IGLJ5*01": 7, "IGLJ6*01": 7, "IGLJ7*01": 7, "IGLJ7*02": 7, "IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ4*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 21, "n_procs": 1, "partition": [["253ca59333-igl"], ["b739ce37b7-igl"], ["aa25e6c0ce-igl"], ["7588f09c07-igl"], ["8807c8ff04-igl"], ["20909c3943-igl"], ["a3baa83300-igl"], ["971ac047ee-igl"], ["a2238f4e9a-igl"], ["8d79fca804-igl"], ["0eb272ee70-igl"], ["09f5010bd3-igl"], ["b02ee7754a-igl"], ["ddcf0ca433-igl"], ["eee6809ad6-igl"], ["14195e4958-igl"], ["d5ddf0c2ec-igl"], ["57537e5f22-igl"], ["b1e56e40a1-igl"], ["21cea6e4d0-igl"], ["4d37fe487e-igl"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["253ca59333-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.014970059880239521], "n_mutations": [5], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["253ca59333-igh", "b739ce37b7-igh", "b739ce37b7-igl"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1445, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b739ce37b7-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["253ca59333-igh", "253ca59333-igl", "b739ce37b7-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 297}, "k_v": {"best": 288, "min": 285, "max": 289}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-23*02": {"score": 1440, "glbounds": [0, 288], "qrbounds": [0, 288]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [288, 288]}}, "j": {"IGLJ1*01": {"score": 190, "glbounds": [0, 38], "qrbounds": [290, 328]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["aa25e6c0ce-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.029940119760479042], "n_mutations": [10], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": 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["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["b1e56e40a1-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1415, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["21cea6e4d0-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "paired-uids": [["21cea6e4d0-igh", "f094dfd68a-igh", "f094dfd68a-igk"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 297, "min": 294, "max": 298}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV2-14*04": {"score": 1485, "glbounds": [0, 297], "qrbounds": [0, 297]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [297, 297]}}, "j": {"IGLJ3*02": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}, "IGLJ2*01": {"score": 165, "glbounds": [3, 38], "qrbounds": [299, 334]}}}], "padlefts": [""], "padrights": [""]}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["4d37fe487e-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.03293413173652695], "n_mutations": [11], "input_seqs": ["TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "paired-uids": [["4d37fe487e-igh"]], "loci": ["igl"], "codon_positions": {"v": 267, "j": 303}, "k_v": {"best": 298, "min": 295, "max": 299}, "k_d": {"best": 1, "min": 1, "max": 2}, "all_matches": [{"v": {"IGLV1-40*01": {"score": 1385, "glbounds": [0, 298], "qrbounds": [0, 298]}}, "d": {"IGLDx-x*x": {"score": 1, "glbounds": [1, 1], "qrbounds": [298, 298]}}, "j": {"IGLJ1*01": {"score": 180, "glbounds": [2, 38], "qrbounds": [298, 334]}}}], "padlefts": [""], "padrights": [""]}]}
test/paired/new-results/test.log CHANGED
@@ -22,18 +22,18 @@ smith-waterman (writing parameters)
22
22
  kept 25 (0.446) unproductive
23
23
  writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
24
24
  writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
25
- water time: 0.7 (ig-sw 0.7 processing 0.0)
25
+ water time: 0.7 (ig-sw 0.6 processing 0.0)
26
26
  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
27
27
  (0.5 sec)
28
28
  hmm
29
29
  reading output
30
30
  read 56 hmm output lines with 56 sequences in 56 events (0 failures)
31
31
  writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
32
- writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
32
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
33
33
  infra time: 1.1
34
34
  hmm step time: 2.1
35
35
  writing hmms removed 3 genes from glfo (leaving v 6 d 15 j 4)
36
- (0.4 sec)
36
+ (0.3 sec)
37
37
  total time: 3.9
38
38
  cache-parameters igk:
39
39
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -70,7 +70,7 @@ hmm
70
70
  infra time: 0.9
71
71
  hmm step time: 1.4
72
72
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
73
- (0.3 sec)
73
+ (0.4 sec)
74
74
  total time: 2.7
75
75
  cache-parameters igl:
76
76
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -106,7 +106,7 @@ hmm
106
106
  hmm step time: 0.9
107
107
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
108
108
  (0.1 sec)
109
- total time: 1.7
109
+ total time: 1.6
110
110
  total time: 12.1
111
111
  partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu
112
112
  warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
@@ -127,7 +127,7 @@ smith-waterman
127
127
  hmm
128
128
  caching all 56 naive sequences (1.0s)
129
129
  collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
130
- 50 clusters with 10 procs (0.6s)
130
+ 50 clusters with 10 procs (0.5s)
131
131
  44 clusters with 7 procs (0.5s)
132
132
  36 clusters with 5 procs (0.4s)
133
133
  31 clusters with 3 procs (0.3s)
@@ -141,7 +141,7 @@ getting annotations for final partition
141
141
  (0.0 sec)
142
142
 
143
143
  subcluster annotation time 0.9
144
- total time: 5.0
144
+ total time: 4.9
145
145
  partition igk:
146
146
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
147
147
  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igk --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -167,7 +167,7 @@ hmm
167
167
  getting annotations for final partition
168
168
  subcluster annotating 6 clusters with steps: (0.3s) (0.1s) (0.1s) plotting performance (0.0 sec)
169
169
 
170
- subcluster annotation time 0.4
170
+ subcluster annotation time 0.5
171
171
  total time: 1.5
172
172
  partition igl:
173
173
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -334,7 +334,7 @@ hmm
334
334
  h 20 --> 23 +3
335
335
  k 6 --> 15 +9
336
336
  l 3 --> 8 +5
337
- total time: 19.8
337
+ total time: 19.7
338
338
  subset-partition-new-simu partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
339
339
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
340
340
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -365,7 +365,7 @@ hmm
365
365
  merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
366
366
  run partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
367
367
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
368
- total time: 68.8
368
+ total time: 67.8
369
369
  seed-partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
370
370
  removing seqs very different from seed seq
371
371
  wrong/no removed singly kept missing
@@ -555,7 +555,7 @@ hmm
555
555
  N clusters with all seqs:
556
556
  h 12 --> 1 -11
557
557
  k 2 --> 1 -1
558
- total time: 9.3
558
+ total time: 9.2
559
559
  get-selection-metrics-new-simu partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
560
560
  get-selection-metrics igh+igk: igh
561
561
  run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -676,10 +676,10 @@ hmm
676
676
  skipped 1/4 clusters that had no uids in common with tree
677
677
  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
678
678
  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
679
- total time: 5.6
679
+ total time: 5.5
680
680
  cache-parameters-data partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
681
681
  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
682
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/641833/meta.yaml --n-max-queries 100
682
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/199071/meta.yaml --n-max-queries 100
683
683
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
684
684
  extract_pairing_info(): read 100 sequences with 48 droplet ids
685
685
  droplet id separators (set automatically): _ indices: [0]
@@ -690,9 +690,9 @@ hmm
690
690
  2 42 0.875
691
691
  3 2 0.042
692
692
  4 2 0.042
693
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/641833 --input-metafname /tmp/runner/hmms/641833/meta.yaml --n-max-queries 100
693
+ run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/199071 --input-metafname /tmp/runner/hmms/199071/meta.yaml --n-max-queries 100
694
694
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
695
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/641833/meta.yaml: paired-uids
695
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/199071/meta.yaml: paired-uids
696
696
  read pairing info for 100 seqs from input meta file
697
697
  running vsearch on 100 sequences:
698
698
  igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -715,10 +715,10 @@ totals: igh 48 igk 37 igl 15
715
715
  2 0.13 h l
716
716
  1 0.07 h k
717
717
  1 0.07 h h k
718
- writing to /tmp/runner/hmms/641833/
719
- igh: 48 to 641833/igh.fa
720
- igk: 37 to 641833/igk.fa
721
- igl: 15 to 641833/igl.fa
718
+ writing to /tmp/runner/hmms/199071/
719
+ igh: 48 to 199071/igh.fa
720
+ igk: 37 to 199071/igk.fa
721
+ igl: 15 to 199071/igl.fa
722
722
  writing to paired subdirs
723
723
  igh+igk:
724
724
  igh: 36 / 48 to igh+igk/igh.fa
@@ -727,8 +727,8 @@ writing to paired subdirs
727
727
  igh: 15 / 48 to igh+igl/igh.fa
728
728
  igl: 15 / 15 to igh+igl/igl.fa
729
729
  cache-parameters igh:
730
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/641833/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/641833/meta.yaml
731
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/641833/meta.yaml: paired-uids
730
+ run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/199071/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/199071/meta.yaml
731
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/199071/meta.yaml: paired-uids
732
732
  caching parameters
733
733
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
734
734
  keeping 23 / 198 v genes
@@ -747,7 +747,7 @@ smith-waterman (writing parameters)
747
747
  writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.0 sec)
748
748
  water time: 2.2 (ig-sw 2.1 processing 0.1)
749
749
  writing hmms removed 13 genes from glfo (leaving v 23 d 19 j 6)
750
- (1.0 sec)
750
+ (0.9 sec)
751
751
  hmm
752
752
  reading output
753
753
  read 48 hmm output lines with 48 sequences in 48 events (0 failures)
@@ -758,8 +758,8 @@ hmm
758
758
  (0.9 sec)
759
759
  total time: 7.5
760
760
  cache-parameters igk:
761
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/641833/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/641833/meta.yaml
762
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/641833/meta.yaml: paired-uids
761
+ run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/199071/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/199071/meta.yaml
762
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/199071/meta.yaml: paired-uids
763
763
  caching parameters
764
764
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
765
765
  keeping 16 / 64 v genes
@@ -775,7 +775,7 @@ smith-waterman (writing parameters)
775
775
  info for 37 / 37 = 1.000 (removed: 0 failed)
776
776
  kept 1 (0.027) unproductive
777
777
  writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
778
- writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.4 sec)
778
+ writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
779
779
  water time: 1.5 (ig-sw 1.4 processing 0.1)
780
780
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
781
781
  (1.0 sec)
@@ -783,14 +783,14 @@ hmm
783
783
  reading output
784
784
  read 37 hmm output lines with 37 sequences in 37 events (0 failures)
785
785
  writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.3 sec)
786
- infra time: 1.4
786
+ infra time: 1.3
787
787
  hmm step time: 1.9
788
788
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
789
789
  (1.0 sec)
790
- total time: 5.7
790
+ total time: 5.6
791
791
  cache-parameters igl:
792
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/641833/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/641833/meta.yaml
793
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/641833/meta.yaml: paired-uids
792
+ run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/199071/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/199071/meta.yaml
793
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/199071/meta.yaml: paired-uids
794
794
  caching parameters
795
795
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
796
796
  keeping 10 / 80 v genes
@@ -804,7 +804,7 @@ smith-waterman (writing parameters)
804
804
  running 10 procs for 15 seqs
805
805
  info for 15 / 15 = 1.000 (removed: 0 failed)
806
806
  writing sw results to test/paired/new-results/test/parameters/data/igl/sw-cache.yaml
807
- writing parameters to test/paired/new-results/test/parameters/data/igl/sw (0.9 sec)
807
+ writing parameters to test/paired/new-results/test/parameters/data/igl/sw (0.8 sec)
808
808
  water time: 0.9 (ig-sw 0.9 processing 0.0)
809
809
  writing hmms removed 6 genes from glfo (leaving v 10 d 1 j 3)
810
810
  (0.6 sec)
@@ -816,6 +816,6 @@ hmm
816
816
  hmm step time: 1.1
817
817
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
818
818
  (0.6 sec)
819
- total time: 3.5
820
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/641833/: failed.fa
821
- total time: 21.9
819
+ total time: 3.4
820
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/199071/: failed.fa
821
+ total time: 21.6