partis-bcr 1.0.10.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11__cp312-cp312-manylinux1_x86_64.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 (42) hide show
  1. {partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.dist-info}/RECORD +42 -42
  3. test/new-results/test.log +3 -3
  4. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  5. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  6. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  7. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  8. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  9. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  10. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  22. test/paired/new-results/run-times.csv +6 -6
  23. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +17 -13
  24. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +6 -2
  25. test/paired/new-results/subset-partition-new-simu/merged-partition.log +10 -6
  26. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  27. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  28. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  29. test/paired/new-results/test.log +47 -38
  30. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/cf-alleles.py +0 -0
  31. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/cf-germlines.py +0 -0
  32. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/compare-plotdirs.py +0 -0
  33. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/extract-pairing-info.py +0 -0
  34. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/gctree-run.py +0 -0
  35. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/get-naive-probabilities.py +0 -0
  36. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/parse-output.py +0 -0
  37. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/partis-test.py +0 -0
  38. {partis_bcr-1.0.10.post1.dev1.data → partis_bcr-1.0.11.data}/scripts/split-loci.py +0 -0
  39. {partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.dist-info}/WHEEL +0 -0
  40. {partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.dist-info}/entry_points.txt +0 -0
  41. {partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.dist-info}/licenses/COPYING +0 -0
  42. {partis_bcr-1.0.10.post1.dev1.dist-info → partis_bcr-1.0.11.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": "b1783efdc4bea09eb047e057f603af1558441dcb", "tag": "v1.0.10", "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": [true], "stops": [true], "paired-uids": [["aa25e6c0ce-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": 1395, "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": ["7588f09c07-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "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": [["7588f09c07-igh", "cb8a759f1a-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": ["8807c8ff04-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": 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["CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["eee6809ad6-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": ["CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [true], "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": [["bc11af4843-igh", "bc11af4843-igk", "eee6809ad6-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": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCA........GCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["14195e4958-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": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true], "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": [false], "stops": [true], "paired-uids": [["14195e4958-igh", "d5ddf0c2ec-igl"]], "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": ["d5ddf0c2ec-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "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": [["14195e4958-igh", "14195e4958-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": 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": ["57537e5f22-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": [["57537e5f22-igh", "7ba384a461-igh", "7ba384a461-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": ["b1e56e40a1-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.023952095808383235], "n_mutations": [8], "input_seqs": ["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
@@ -21,9 +21,9 @@ smith-waterman (writing parameters)
21
21
  kept 25 (0.446) unproductive
22
22
  writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
23
23
  writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
24
- water time: 0.7 (ig-sw 0.7 processing 0.0)
24
+ water time: 0.7 (ig-sw 0.6 processing 0.0)
25
25
  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
26
- (0.6 sec)
26
+ (0.5 sec)
27
27
  hmm
28
28
  reading output
29
29
  read 56 hmm output lines with 56 sequences in 56 events (0 failures)
@@ -32,7 +32,7 @@ hmm
32
32
  infra time: 1.1
33
33
  hmm step time: 2.2
34
34
  writing hmms removed 3 genes from glfo (leaving v 6 d 15 j 4)
35
- (0.3 sec)
35
+ (0.4 sec)
36
36
  total time: 4.0
37
37
  cache-parameters igk:
38
38
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -69,7 +69,7 @@ hmm
69
69
  hmm step time: 1.4
70
70
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
71
71
  (0.4 sec)
72
- total time: 2.8
72
+ total time: 2.7
73
73
  cache-parameters igl:
74
74
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
75
75
  run partis cache-parameters --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -103,8 +103,8 @@ hmm
103
103
  hmm step time: 0.9
104
104
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
105
105
  (0.1 sec)
106
- total time: 1.7
107
- total time: 12.4
106
+ total time: 1.6
107
+ total time: 12.2
108
108
  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
109
109
  warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
110
110
  partition igh:
@@ -124,7 +124,7 @@ smith-waterman
124
124
  hmm
125
125
  caching all 56 naive sequences (1.1s)
126
126
  collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
127
- 50 clusters with 10 procs (0.6s)
127
+ 50 clusters with 10 procs (0.5s)
128
128
  44 clusters with 7 procs (0.5s)
129
129
  36 clusters with 5 procs (0.4s)
130
130
  31 clusters with 3 procs (0.3s)
@@ -187,7 +187,7 @@ hmm
187
187
  3 clusters with 1 proc (0.1s)
188
188
  partition loop time: 0.2
189
189
  getting annotations for final partition
190
- subcluster annotating 3 clusters with steps: (0.2s) (0.1s) (0.1s) plotting performance (0.0 sec)
190
+ subcluster annotating 3 clusters with steps: (0.1s) (0.1s) (0.1s) plotting performance (0.0 sec)
191
191
 
192
192
  subcluster annotation time 0.3
193
193
  total time: 0.9
@@ -228,6 +228,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
228
228
  joint 0.963 0.594
229
229
  merge time 0.0
230
230
  need to get annotations for 7/15 joint igh clusters
231
+ tag: v1.0.11
231
232
  annotate igh+igk: igh
232
233
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
233
234
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
@@ -245,6 +246,7 @@ hmm
245
246
  subcluster annotation time 0.6
246
247
  total time: 0.6
247
248
  need to get annotations for 13/15 joint igk clusters
249
+ tag: v1.0.11
248
250
  annotate igh+igk: igk
249
251
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
250
252
  run partis annotate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igk.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
@@ -260,7 +262,7 @@ smith-waterman
260
262
  hmm
261
263
  subcluster annotating 15 clusters with steps: (0.3s) (0.1s)
262
264
  subcluster annotation time 0.4
263
- total time: 0.5
265
+ total time: 0.4
264
266
  igh+igl: synchronizing heavy and light chain cluster paths
265
267
  removing badly + unpaired seqs: kept 7 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 3 l 4
266
268
  note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -286,6 +288,7 @@ hmm
286
288
  joint 1.000 0.611
287
289
  merge time 0.0
288
290
  need to get annotations for 5/8 joint igh clusters
291
+ tag: v1.0.11
289
292
  annotate igh+igl: igh
290
293
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
291
294
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
@@ -303,6 +306,7 @@ hmm
303
306
  subcluster annotation time 0.4
304
307
  total time: 0.5
305
308
  need to get annotations for 8/8 joint igl clusters
309
+ tag: v1.0.11
306
310
  annotate igh+igl: igl
307
311
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
308
312
  run partis annotate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igl.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
@@ -331,7 +335,7 @@ hmm
331
335
  h 20 --> 23 +3
332
336
  k 6 --> 15 +9
333
337
  l 3 --> 8 +5
334
- total time: 20.9
338
+ total time: 19.9
335
339
  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
336
340
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
337
341
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -360,9 +364,12 @@ hmm
360
364
  writing merged outputs from 2 subsets to test/paired/new-results/subset-partition-new-simu/merged-subsets
361
365
  writing combined h/l info to fasta and meta files in test/paired/new-results/subset-partition-new-simu/merged-subsets
362
366
  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
367
+ tag: v1.0.11
368
+ tag: v1.0.11
369
+ tag: v1.0.11
363
370
  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
364
371
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
365
- total time: 71.1
372
+ total time: 68.2
366
373
  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
367
374
  removing seqs very different from seed seq
368
375
  wrong/no removed singly kept missing
@@ -400,7 +407,7 @@ getting annotations for final partition
400
407
  reading output
401
408
  read 12 hmm output lines with 17 sequences in 12 events (0 failures)
402
409
  hmm step time: 0.3
403
- total time: 2.0
410
+ total time: 1.9
404
411
  partition igk:
405
412
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
406
413
  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/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
@@ -423,7 +430,7 @@ hmm
423
430
  getting annotations for final partition
424
431
  subcluster annotating 2 clusters with steps: (0.1s) (0.1s) (0.1s)
425
432
  subcluster annotation time 0.2
426
- total time: 0.6
433
+ total time: 0.7
427
434
  partition igl:
428
435
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
429
436
  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igl.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -485,6 +492,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
485
492
  merge time 0.0
486
493
  removed 7 unseeded clusters (of 8 total, leaving 1) from igh joint partition
487
494
  seed cluster size in best joint partition: 1, excluding seed seq: 0
495
+ tag: v1.0.11
488
496
  annotate igh+igk: igh
489
497
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
490
498
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -506,6 +514,7 @@ hmm
506
514
  removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
507
515
  need to get annotations for 1/1 joint igk clusters
508
516
  seed cluster size in best joint partition: 1, excluding seed seq: 0
517
+ tag: v1.0.11
509
518
  annotate igh+igk: igk
510
519
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
511
520
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -552,7 +561,7 @@ hmm
552
561
  N clusters with all seqs:
553
562
  h 12 --> 1 -11
554
563
  k 2 --> 1 -1
555
- total time: 9.5
564
+ total time: 9.3
556
565
  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
557
566
  get-selection-metrics igh+igk: igh
558
567
  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
@@ -632,7 +641,7 @@ hmm
632
641
  starting 2 jobs
633
642
  run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/input-seqs.fa
634
643
  run /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/input-seqs.fa
635
- made 2 fasttree trees (0.1s)
644
+ made 2 fasttree trees (0.0s)
636
645
  tree origins: 2 ran fasttree
637
646
  setting default tau to 1 / 334 = 0.0030
638
647
  calculating normalized lb index and lb ratio and lb fraction with tau 0.0030
@@ -673,10 +682,10 @@ hmm
673
682
  skipped 1/4 clusters that had no uids in common with tree
674
683
  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
675
684
  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
676
- total time: 5.8
685
+ total time: 5.6
677
686
  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
678
687
  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
679
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/400051/meta.yaml --n-max-queries 100
688
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/275115/meta.yaml --n-max-queries 100
680
689
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
681
690
  extract_pairing_info(): read 100 sequences with 48 droplet ids
682
691
  droplet id separators (set automatically): _ indices: [0]
@@ -687,9 +696,9 @@ hmm
687
696
  2 42 0.875
688
697
  3 2 0.042
689
698
  4 2 0.042
690
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/400051 --input-metafname /tmp/runner/hmms/400051/meta.yaml --n-max-queries 100
699
+ run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/275115 --input-metafname /tmp/runner/hmms/275115/meta.yaml --n-max-queries 100
691
700
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
692
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
701
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
693
702
  read pairing info for 100 seqs from input meta file
694
703
  running vsearch on 100 sequences:
695
704
  igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -712,10 +721,10 @@ totals: igh 48 igk 37 igl 15
712
721
  2 0.13 h l
713
722
  1 0.07 h k
714
723
  1 0.07 h h k
715
- writing to /tmp/runner/hmms/400051/
716
- igh: 48 to 400051/igh.fa
717
- igk: 37 to 400051/igk.fa
718
- igl: 15 to 400051/igl.fa
724
+ writing to /tmp/runner/hmms/275115/
725
+ igh: 48 to 275115/igh.fa
726
+ igk: 37 to 275115/igk.fa
727
+ igl: 15 to 275115/igl.fa
719
728
  writing to paired subdirs
720
729
  igh+igk:
721
730
  igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +733,8 @@ writing to paired subdirs
724
733
  igh: 15 / 48 to igh+igl/igh.fa
725
734
  igl: 15 / 15 to igh+igl/igl.fa
726
735
  cache-parameters igh:
727
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/400051/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/400051/meta.yaml
728
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
736
+ run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
737
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
729
738
  caching parameters
730
739
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
731
740
  keeping 23 / 198 v genes
@@ -752,11 +761,11 @@ hmm
752
761
  infra time: 2.0
753
762
  hmm step time: 3.0
754
763
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
755
- (0.9 sec)
764
+ (1.0 sec)
756
765
  total time: 7.5
757
766
  cache-parameters igk:
758
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/400051/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/400051/meta.yaml
759
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
767
+ run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
768
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
760
769
  caching parameters
761
770
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
762
771
  keeping 16 / 64 v genes
@@ -775,7 +784,7 @@ smith-waterman (writing parameters)
775
784
  writing parameters to test/paired/new-results/test/parameters/data/igk/sw (1.3 sec)
776
785
  water time: 1.5 (ig-sw 1.4 processing 0.1)
777
786
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
778
- (1.1 sec)
787
+ (1.0 sec)
779
788
  hmm
780
789
  reading output
781
790
  read 37 hmm output lines with 37 sequences in 37 events (0 failures)
@@ -783,11 +792,11 @@ hmm
783
792
  infra time: 1.3
784
793
  hmm step time: 1.9
785
794
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
786
- (1.1 sec)
787
- total time: 5.8
795
+ (1.0 sec)
796
+ total time: 5.7
788
797
  cache-parameters igl:
789
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/400051/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/400051/meta.yaml
790
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/400051/meta.yaml: paired-uids
798
+ run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
799
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
791
800
  caching parameters
792
801
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
793
802
  keeping 10 / 80 v genes
@@ -804,7 +813,7 @@ smith-waterman (writing parameters)
804
813
  writing parameters to test/paired/new-results/test/parameters/data/igl/sw (0.9 sec)
805
814
  water time: 0.9 (ig-sw 0.9 processing 0.0)
806
815
  writing hmms removed 6 genes from glfo (leaving v 10 d 1 j 3)
807
- (0.7 sec)
816
+ (0.6 sec)
808
817
  hmm
809
818
  reading output
810
819
  read 15 hmm output lines with 15 sequences in 15 events (0 failures)
@@ -812,7 +821,7 @@ hmm
812
821
  infra time: 0.8
813
822
  hmm step time: 1.1
814
823
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
815
- (0.7 sec)
816
- total time: 3.6
817
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/400051/: failed.fa
818
- total time: 22.1
824
+ (0.6 sec)
825
+ total time: 3.5
826
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/275115/: failed.fa
827
+ total time: 21.8