PyPI - partis-bcr - Versions diffs - 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl - Mend

partis-bcr 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__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.

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test/new-results/test/simu.yaml ADDED Viewed

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+ {"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": 0.0, "n_clusters": 10, "n_procs": 1, "partition": [["fc846a4540", "f977acb49b", "9a4254e968"], ["e883678985", "d3487934e0", "2ded5892c4", "2ed5fb6457", "19458e6805", "0ee3136ea7", "279a8071f5", "e004ac921a", "ec4aa1d63b"], ["52a4cc50e5"], ["081307416c", "91796617a0", "4233d708fe", "a484f584e9", "13de8675ec", "33aaa62e12", "31e052ee14"], ["226be79d5f", "188e1a0235"], ["eeca70ed28", "c7a8a5b2f0", "b2982a29ea", "d9172b4f22", "27eccd7baf", "21f0e10a44", "64de54c978", "579bc5aa80"], ["f29bce4695", "36d80d25ae"], ["d024e5cab0", "822801f8ab"], ["c19efdaf0d"], ["5f7b69c48f"]]}], "events": [{"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "reco_id": "5611db2b0a", "tree": "[&R] (((fc846a4540:0.011735241311499707,f977acb49b:0.011735241311499707)fhu:0.000596485808076228,9a4254e968:0.012331727121575934)fty:0.006419249533820349)ael:0.0;\n", "unique_ids": ["fc846a4540", "f977acb49b", "9a4254e968"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mut_freqs": [0.026385224274406333, 0.023746701846965697, 0.021108179419525065], "n_mutations": [10, 9, 8], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTTGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAAGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTAAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGTGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGTAGCTGGTACCTATTGTAAGTTACGTGAGGGTATGGACGTCTGGGGCCAAGGGAACACGGTCACCGTCTCCTCAG", "GAGGTGCACCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGAATGAGCTGGGTCCGCCAGGCTCCAGGGAAAAGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAATGAGAAATACTATGTGGACTCTATGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCTTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTGTAACTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCATCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAAGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGGAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTACTACTGTGCGAGAGACTGCGAAGCAGGTGGTACCTATTGTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, false], "loci": ["igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 345}}, {"qr_gap_seqs": ["", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", ""], "reco_id": "fbdf4feea6", "tree": "[&R] (((19458e6805:0.015182952109610126,((ec4aa1d63b:0.012757629919672404,(279a8071f5:0.0002717575583930217,(e004ac921a:0.0001314647675966242,e883678985:0.0001314647675966242)cpu:0.00014029279079639753)cqx:0.012485872369679383)aru:0.002397661445938432,2ed5fb6457:0.015155291369610838)lqs:2.766074313928972e-05)fhp:0.002232979424942661,(d3487934e0:0.01469171558962274,(0ee3136ea7:0.0051119153638687345,2ded5892c4:0.0051119153638687345)duw:0.009579800227754006)irt:0.002724215945930047)pqz:0.0013350451159657181)ahx:0.0;\n", "unique_ids": ["e883678985", "d3487934e0", "2ded5892c4", "2ed5fb6457", "19458e6805", "0ee3136ea7", "279a8071f5", "e004ac921a", "ec4aa1d63b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.002890173410404624, 0.023121387283236993, 0.017341040462427744, 0.017341040462427744, 0.014450867052023121, 0.02601156069364162, 0.002890173410404624, 0.002890173410404624, 0.008670520231213872], "n_mutations": [1, 8, 6, 6, 5, 9, 1, 1, 3], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGGGGTCTCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTTCGTGAAGGGCCGATTGACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGTGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAA", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTTACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATTGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGGTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCTAGGGATCCCTGGTCACCGTCTCCTCAA", "GAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGCCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTAAAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCACCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCAGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGACTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTCCAGCCTCTCGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTATATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTACGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "TAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTTACCGTCAGTAGCAACTATATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATTGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGCCAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCCACTACTGGGGCTAGGGATCCCTGGTCACCGTCTCCTCAA", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCTTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTAGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true], "stops": [false, false, true, true, false, true, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "reco_id": "a5090d8abc", "tree": "[&R] (52a4cc50e5:0.013345547850351035)cqu:0.0;\n", "unique_ids": ["52a4cc50e5"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.027700831024930747], "n_mutations": [10], "input_seqs": ["CAAGTGCAACTGCAGGAGTCGGGCCGAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTAGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACCTCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACCGCCGCAGACACGGCCATATATTACTGTGCGAGTTATTTGCTCGGGTACAGCAGCAGAGCCCCTGTCTACTGGGGCCAGCGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCCTGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "loci": ["igh"], "codon_positions": {"v": 282, "j": 327}}, {"qr_gap_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCT.......GAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "reco_id": "9dacfa8deb", "tree": "[&R] ((081307416c:0.002623905430250834,(((33aaa62e12:0.0018644309441782313,(4233d708fe:0.0007456991718712855,91796617a0:0.0007456991718712855)bcq:0.0011187317721069456)cgu:0.0003440212853328869,a484f584e9:0.002208452229211118)dtz:0.0002014382533192566,(13de8675ec:0.0006150090664587922,31e052ee14:0.0006150090664587922)hty:0.0017948814161715826)bik:0.00021401494702045888)kqu:2.6274006232511675e-05)evz:0.0;\n", "unique_ids": ["081307416c", "91796617a0", "4233d708fe", "a484f584e9", "13de8675ec", "33aaa62e12", "31e052ee14"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mut_freqs": [0.008174386920980926, 0.0, 0.0, 0.0027247956403269754, 0.0, 0.0, 0.0], "n_mutations": [3, 0, 0, 1, 0, 0, 0], "input_seqs": ["CAGGTTCAGCTGGTGCAATCTGGAGCTGAGGTGTAGAAGCTTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAACAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, true, true], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "CTTCCCTT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, false, true], "stops": [true, false, false, false, false, true, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 285, "j": 333}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "f220c52535", "tree": "[&R] ((226be79d5f:0.001583152227990051,188e1a0235:0.001583152227990051)hmq:0.0010670272079932946)afh:0.0;\n", "unique_ids": ["226be79d5f", "188e1a0235"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCGGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAAAACCAGTTCTCGCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGA.....GTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGTCCAGGACTGATGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGCGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCGCCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCA............GCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAAAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCATTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "", "", "", ""], "gl_gap_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTT....CCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", ""], "indel_reversed_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCGGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAAAACCAGTTCTCGCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "CAGGTGCAGCTGCAGGAGTCGGGTCCAGGACTGATGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGCGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCGCCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGGAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAAAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "", "", "", ""], "reco_id": "e19f613502", "tree": "[&R] (((c7a8a5b2f0:0.011473947230957373,(d9172b4f22:0.011204353580934877,((64de54c978:0.007472444634623492,(b2982a29ea:0.0026644178012223156,21f0e10a44:0.0026644178012223156)lpv:0.004808026833401175)nvx:0.0024335773692030545,(eeca70ed28:0.0016674331281391287,579bc5aa80:0.0016674331281391287)dop:0.008238588875687418)jvx:0.0012983315721083314)inp:0.0002695936561224946)dln:0.0004813332009401619,27eccd7baf:0.011955280430997533)hop:0.0013902674171160023)lmw:0.0;\n", "unique_ids": ["eeca70ed28", "c7a8a5b2f0", "b2982a29ea", "d9172b4f22", "27eccd7baf", "21f0e10a44", "64de54c978", "579bc5aa80"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mut_freqs": [0.013192612137203167, 0.010554089709762533, 0.018469656992084433, 0.018469656992084433, 0.010554089709762533, 0.021108179419525065, 0.005277044854881266, 0.018469656992084433], "n_mutations": [5, 4, 7, 7, 4, 8, 2, 7], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGCAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGGCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGGATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCGGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAAAACCAGTTCTCGCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGGTTATTACTACGAATACTTCCAGCATTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGCGTATATCTATTACAGTGGGAGCACTAACTACAACCCCTCCCTGAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGGGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGTCCAGGACTGATGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGCGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCGCCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAAAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCATTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTATCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATCACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTTCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGTACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAATCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACTAACTACCACCCCTCCCTGAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGGGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGCCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGGGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTTGGGCCCAGGACTGGTGAAGCCTTCGCAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGTTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGGCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGGATACTTCCAGCACTGGGGCCAGGGCACCCTGGCCACCGTCTCCTCAG"], "has_shm_indels": [false, true, false, true, false, false, false, false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], []], "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, true, false, false, false, false], "in_frames": [true, false, true, true, true, true, true, true], "stops": [false, true, false, false, false, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 345}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "a7dd2ff3bf", "tree": "[&R] ((f29bce4695:0.0007728403427523895,36d80d25ae:0.0007728403427523895)bin:0.012572707507598646)glt:0.0;\n", "unique_ids": ["f29bce4695", "36d80d25ae"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mut_freqs": [0.008522727272727272, 0.008522727272727272], "n_mutations": [3, 3], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGAGCCGATTCACCATCTCTAGAGACAATTCCAAGGACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGAGCCGATTCACCATCTCTAGAGACAATTCCAAGGACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 7, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "GTCTCAGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 282, "j": 318}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "reco_id": "962999a75d", "tree": "[&R] ((d024e5cab0:-0.0,822801f8ab:-0.0)dkw:-0.0)agk:0.0;\n", "unique_ids": ["d024e5cab0", "822801f8ab"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "reco_id": "91f77d882f", "tree": "[&R] (c19efdaf0d:0.018750976654062952)ios:0.0;\n", "unique_ids": ["c19efdaf0d"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.019230769230769232], "n_mutations": [7], "input_seqs": ["GAGGTGCAGCTTGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTATTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGACTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCATGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGGCGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTAGTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "loci": ["igh"], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "reco_id": "256bc9b5ab", "tree": "[&R] (5f7b69c48f:0.018750976654062952)efl:0.0;\n", "unique_ids": ["5f7b69c48f"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mut_freqs": [0.016216216216216217], "n_mutations": [6], "input_seqs": ["GAGGTGCAGCTGGTGTAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGCGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCATTAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCAGCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 6, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAG", "dj_insertion": "AGGGCGCCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "loci": ["igh"], "codon_positions": {"v": 282, "j": 336}}]}

test/new-results/test.log CHANGED Viewed

@@ -1,30 +1,279 @@
-[92mcache-parameters-quick-new-simu[0m   partis cache-parameters --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --n-max-queries 10 --random-seed 1 --n-procs 10
-  --n-max-queries: stopped after reading 10 queries from input file
+[92mcache-parameters-simu[0m            partis cache-parameters --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --is-simu --random-seed 1 --n-procs 10
 caching parameters
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.0 sec
-    keeping 2 / 198 v genes
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+    keeping 7 / 198 v genes
+    [91mmissing[0m 8 simulation genes (counts): [95mh[0m[91mv[0m[95m1[0m[95m-2[0m[93m02[0m 0  [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m02[0m 0  [95mh[0m[91mv[0m[95m2[0m[95m-70D[0m[93m04[0m 0  [95mh[0m[91mv[0m[95m3[0m[95m-11[0m[93m04[0m 0  [95mh[0m[91mv[0m[95m3[0m[95m-69-1[0m[93m02[0m 0  [95mh[0m[91mv[0m[95m3[0m[95m-9[0m[93m02[0m 0  [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m 0  [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m09[0m 0
 smith-waterman  (new-allele fitting)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.0 sec
-    running 10 procs for 10 seqs
-      info for 10 / 10 = 1.000   (removed: 0 failed)
-      kept 10 (1.000) unproductive
-    water time: 0.0  (ig-sw 0.0  processing 0.0)
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+  removing old sw cache test/new-results/test/parameters/simu/sw-cache.yaml
+    running 10 procs for 36 seqs
+    running 11 procs for 1 seq
+      info for 36 / 36 = 1.000   (removed: 0 failed)
+      kept 18 (0.500) unproductive
+    water time: 0.1  (ig-sw 0.0  processing 0.0)
 smith-waterman  (writing parameters)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.0 sec
-    running 10 procs for 10 seqs
-      info for 10 / 10 = 1.000   (removed: 0 failed)
-      kept 10 (1.000) unproductive
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+    running 10 procs for 36 seqs
+    running 11 procs for 1 seq
+      info for 36 / 36 = 1.000   (removed: 0 failed)
+      kept 18 (0.500) unproductive
         writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
-    writing parameters to test/new-results/test/parameters/simu/sw (1.3 sec)
-    water time: 1.3  (ig-sw 1.3  processing 0.0)
-  writing hmms     removed 35 genes from glfo (leaving v 2  d 1  j 2)
-(0.1 sec)
+    writing parameters to test/new-results/test/parameters/simu/sw (0.7 sec)
+    water time: 0.8  (ig-sw 0.7  processing 0.0)
+  writing hmms     removed 30 genes from glfo (leaving v 7  d 5  j 3)
+(0.5 sec)
 hmm
     reading output
-        read 10 hmm output lines with 10 sequences in 10 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/simu/hmm (0.2 sec)
-         infra time: 0.2
-      hmm step time: 0.4
-  writing hmms     removed 0  genes from glfo (leaving v 2  d 1  j 2)
-(0.1 sec)
-      total time: 2.1
+        read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
+    writing parameters to test/new-results/test/parameters/simu/hmm (0.6 sec)
+    writing parameters to test/new-results/test/parameters/simu/true (0.6 sec)
+         infra time: 1.3
+      hmm step time: 1.9
+  writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
+(0.5 sec)
+      total time: 3.9
+[92mannotate-new-simu[0m                partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --is-simu --plotdir test/new-results/annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/annotate-new-simu.yaml
+annotating    (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+  plotting performance
+    [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+        water time: 0.1
+hmm
+    reading output
+        read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
+  plotting performance
+    [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+      hmm step time: 0.6
+      total time: 0.7
+[92mmulti-annotate-new-simu[0m          partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --simultaneous-true-clonal-seqs --is-simu --plotdir test/new-results/multi-annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/multi-annotate-new-simu.yaml
+annotating    (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+  note: not running msa indel stuff for --simultaneous-true-clonal-seqs, so any families with shm indels within cdr3 will be split up before running the hmm. To fix this you'll either need to run set_msa_info() (which is fine and easy, but slow, and requires deciding whether to make sure to run parameter caching with the arg, or else rerun smith waterman with the msa indels
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+  plotting performance
+    [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+        water time: 0.1
+hmm
+  --simultaneous-true-clonal-seqs: grouping seqs according to true partition
+  [93mwarning[0m split apart 1 cluster that contained multiple cdr3 lengths (total clusters: 10 --> 11)
+      cluster splits:   8 --> 7 1
+  subcluster annotating 11 clusters with steps:  (0.3s) (0.1s)   plotting performance
+    [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+    subcluster annotation time 0.5
+      total time: 0.6
+[92mpartition-new-simu[0m               partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --plotdir test/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml
+partitioning     (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+  plotting performance
+    [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+        water time: 0.1
+hmm
+  --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
+  caching all 36 naive sequences (0.6s)
+    collapsed 36 queries into 12 clusters with identical naive seqs (0.0 sec)
+  12 clusters with 10 procs (0.0s)
+   12 clusters with 7 procs (0.0s)
+   12 clusters with 5 procs (0.0s)
+   12 clusters with 3 procs (0.0s)
+   12 clusters with 2 procs (0.1s)
+   11 clusters with 1 proc (0.3s)
+       partition loop time: 0.6
+getting annotations for final partition
+  subcluster annotating 10 clusters with steps:  (0.3s) (0.1s) (0.1s)   plotting performance
+    [93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+    subcluster annotation time 0.5
+      total time: 1.8
+[92mseed-partition-new-simu[0m          partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --seed-unique-id 8024ed1a22 --random-seed 1 --n-procs 10 --outfname test/new-results/seed-partition-new-simu.yaml
+partitioning     (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+      removed 25 / 36 = 0.69 sequences with cdr3 length different from seed sequence (leaving 11)
+        water time: 0.0
+hmm
+  --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
+   collapsed 11 queries into 2 clusters with identical naive seqs (0.0 sec)
+  reducing n procs to number of clusters: 10 --> 2
+  2 clusters with 2 procs (0.0s)
+       removed 0 sequences in unseeded clusters, split 2 seeded clusters into 11 singletons, and merged these into 2 clusters with identical naive seqs (0.0 sec)
+        new n_procs 1 (initial seqs/proc: 5.50   new seqs/proc: 2.00
+  2 clusters with 1 proc (0.1s)
+       partition loop time: 0.1
+getting annotations for final partition
+  subcluster annotating 1 cluster with steps:  (0.1s) (0.1s) (0.1s)
+    subcluster annotation time 0.2
+  seed cluster size in best partition: 11, excluding seed seq: 10
+      total time: 0.4
+[92mvsearch-partition-new-simu[0m       partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --naive-vsearch --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --random-seed 1 --n-procs 10 --outfname test/new-results/vsearch-partition-new-simu.yaml
+partitioning     (with test/new-results/test/parameters/simu/hmm)
+smith-waterman
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.0 sec
+        reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
+      info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
+      kept 18 (0.500) unproductive
+        water time: 0.0
+hmm
+  --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
+        collapsed 36 sequences (36 initial naive seqs/clusters) into 12 unique naive sequences over 9 cdr3 lengths (0.0 sec)
+    using hfrac bound for vsearch 0.013
+    running vsearch 9 times (once for each cdr3 length class): . . . . . . . . .
+      vsearch time: 0.1
+getting annotations for final partition
+      calculating hmm annotations even though --fast/--naive-vsearch was set (you can set --use-sw-annotations to get faster (but substantially less accurate) annotations, or set --dont-calculate-annotations if you only need the partition)
+  subcluster annotating 10 clusters with steps:  (0.3s) (0.1s) (0.1s)
+    subcluster annotation time 0.5
+      total time: 0.6
+[92mget-selection-metrics-new-simu[0m   partis get-selection-metrics --dont-write-git-info --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml --selection-metric-fname test/new-results/get-selection-metrics-new-simu.yaml
+  note: --parameter-dir not set, so using default: x-dummy-x
+  note: By default we print/operate on *all* annotations in the output file, which in general can include annotations from non-best partititons and non-seed clusters (e.g. if --n-final-clusters was set).
+        If you want to restrict to particular annotations, use one of --only-print-best-partition, --only-print-seed-clusters, or --only-print-queries-to-include-clusters (or, if set during partitioning, --n-final-clusters or --min-largest-cluster-size).
+    getting selection metrics (lbi lbr aa-lbi aa-lbr cons-dist-aa) with inferred lines: 4 clusters with sizes 11 7 7 3
+      skipped 6 smaller than 3 (controlled by --min-selection-metric-cluster-size)
+    getting trees for 3 clusters with sizes: 11 7 7
+      starting 3 jobs
+        [91mrun[0m /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+        [91mrun[0m /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+        [91mrun[0m /home/runner/work/partis/partis/bin/FastTree-linux -gtr -nt -out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out /home/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+      made 3 fasttree trees (0.1s)
+    tree origins: 3 ran fasttree
+    skipped 1/4 clusters smaller than 4
+      setting default tau to 1 / 352 = 0.0028
+    calculating normalized lb index and lb ratio and lb fraction with tau 0.0028
+      [93mwarning[0m get_aa_tree() (AA inf tree, iclust 0): skipped 13/18 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: amz bev bnw bop dkn ikm
+      setting default tau to 1 / 352 = 0.0028
+    calculating normalized lb index and lb ratio and lb fraction on aa tree with tau 0.0028
+                [94miclust 1: [0m[93mwarning [0mtree depth and mfreq differ by more than 25% for 2/7 nodes (note that this is expected if these are single chain sequences being compared to a paired h+l tree)
+                    mean values:  tree depth 0.001  mfreq 0.001  diff 0.000  abs(frac diff) 25%  ratio 1.3
+          10 with highest abs(diff):
+            tree depth   mfreq      ratio    diff
+              0.0034    0.0027       1.3     0.0007     20a0129b57
+              0.0034    0.0027       1.3     0.0007     97366cf0d8
+          10 with highest+lowest ratios:
+              0.0034    0.0027       1.3     0.0007     20a0129b57
+              0.0034    0.0027       1.3     0.0007     97366cf0d8
+              0.0034    0.0027       1.3     0.0007     20a0129b57
+              0.0034    0.0027       1.3     0.0007     97366cf0d8
+      [93mwarning[0m get_aa_tree() (AA inf tree, iclust 1): skipped 3/9 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: eov
+      [93mwarning[0m get_aa_tree() (AA inf tree, iclust 2): skipped 11/13 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: apr dhq fnv nox uvx
+    skipped 1/4 clusters that had no uids in common with tree
+  writing selection metrics to test/new-results/get-selection-metrics-new-simu.yaml
+      total time: 0.1
+[92mcache-parameters-data[0m            partis cache-parameters --dont-write-git-info --infname test/mishmash.fa --parameter-dir test/new-results/test/parameters/data --sw-cachefname test/new-results/test/parameters/data/sw-cache.yaml --n-max-queries 50 --input-metafnames test/input-meta.yaml --random-seed 1 --n-procs 10
+    stopped after reading 50 sequences from test/mishmash.fa
+  --n-max-queries: stopped after reading 50 queries from input file
+  --input-metafnames: added meta info for 4 sequences from test/input-meta.yaml: multiplicities
+caching parameters
+  vsearch: 44 / 50 v annotations (6 failed) with 54 v genes in 0.0 sec
+    keeping 24 / 198 v genes
+smith-waterman  (new-allele fitting)
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.0 sec
+    running 10 procs for 50 seqs
+    running 12 procs for 5 seqs
+      info for 46 / 50 = 0.920   (removed: 4 failed)
+      kept 16 (0.320) unproductive
+    water time: 0.1  (ig-sw 0.0  processing 0.0)
+smith-waterman  (writing parameters)
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.0 sec
+    running 10 procs for 46 seqs
+    running 11 procs for 1 seq
+      info for 46 / 50 = 0.920   (removed: 4 failed)
+      kept 16 (0.320) unproductive
+        writing sw results to test/new-results/test/parameters/data/sw-cache.yaml
+    writing parameters to test/new-results/test/parameters/data/sw (0.8 sec)
+    water time: 1.0  (ig-sw 0.9  processing 0.0)
+  writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
+(0.8 sec)
+hmm
+    reading output
+        read 46 hmm output lines with 46 sequences in 46 events  (0 failures)
+    writing parameters to test/new-results/test/parameters/data/hmm (0.7 sec)
+         infra time: 0.8
+      hmm step time: 2.2
+  writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
+(0.7 sec)
+      total time: 4.9
+[92msimulate[0m                         partis simulate --dont-write-git-info --parameter-dir test/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --no-per-base-mutation --random-seed 1 --n-procs 10 --outfname test/new-results/test/simu.yaml --indel-frequency 0.2
+simulating
+      --> proc 0
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 5.6
+      --> proc 1
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 5.8
+      --> proc 2
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 5.9
+      --> proc 3
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 7 seqs in 0.2s (0.0s of which was running bppseqgen)
+      total time: 5.7
+      --> proc 4
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 6.0
+      --> proc 5
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 8 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 5.9
+      --> proc 6
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 5.9
+      --> proc 7
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 5.8
+      --> proc 8
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 5.4
+      --> proc 9
+    reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 1 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 5.7
+   read 10 events with 36 seqs from 10 .yaml files
+      total time: 11.4

test/new-results/vsearch-partition-new-simu.yaml ADDED Viewed

@@ -0,0 +1 @@

+ {"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": 0.0, "n_clusters": 10, "n_procs": 1, "partition": [["16df39683f", "7f6d2ba874", "6e208eca11"], ["8024ed1a22", "18f4019708", "ee25049b92", "efdea248af", "5fb484a8a6", "648902c3e5", "f47122f1f5", "308de1d739", "d024e5cab0", "822801f8ab", "9c3cedb840"], ["e64fcd9e03"], ["401a542698"], ["20a0129b57", "91796617a0", "4233d708fe", "97366cf0d8", "13de8675ec", "33aaa62e12", "31e052ee14"], ["226be79d5f", "188e1a0235"], ["bf50fa2017", "73d6c6e558", "162cb1691f", "c8a90cc3d7", "17f57acf2e", "948b83fb4d", "73431a9b10"], ["d8761c689a"], ["93c01dd961", "c761732a8b"], ["adc41b4237"]], "ccf_under": 0.9090909090909087, "ccf_over": 0.9513888888888888, "perf_metrics": {}, "n_true_clusters": 10}], "events": [{"has_shm_indels": [false, false, false, false, false, false, false, false, false, false, false], "qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "unique_ids": ["8024ed1a22", "18f4019708", "ee25049b92", "efdea248af", "5fb484a8a6", "648902c3e5", "f47122f1f5", "308de1d739", "d024e5cab0", "822801f8ab", "9c3cedb840"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mut_freqs": [0.011560693641618497, 0.02023121387283237, 0.023121387283236993, 0.014450867052023121, 0.02023121387283237, 0.011560693641618497, 0.011560693641618497, 0.017341040462427744, 0.0, 0.0, 0.02023121387283237], "n_mutations": [4, 7, 8, 5, 7, 4, 4, 6, 0, 0, 7], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999990466130269, "IGHD6-19*01": 9.533869773964565e-07}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, true, true, true, false, false, true], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 318}}, {"has_shm_indels": [false, false, false, false, false, true, true], "qr_gap_seqs": ["", "", "", "", "", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "", "", "", "", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGC.......TGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "", "", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["20a0129b57", "91796617a0", "4233d708fe", "97366cf0d8", "13de8675ec", "33aaa62e12", "31e052ee14"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mut_freqs": [0.0027247956403269754, 0.0, 0.0, 0.0027247956403269754, 0.0, 0.0, 0.0], "n_mutations": [1, 0, 0, 1, 0, 0, 0], "input_seqs": ["NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999999994316, "IGHD6-19*01": 5.698073919757748e-13}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 5, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "TCCCT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 336}}, {"has_shm_indels": [false, true, false, false, false, false, false], "qr_gap_seqs": ["", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATG.....AGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", "", ""], "gl_gap_seqs": ["", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", "", ""], "indel_reversed_seqs": ["", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", "", "", ""], "unique_ids": ["bf50fa2017", "73d6c6e558", "162cb1691f", "c8a90cc3d7", "17f57acf2e", "948b83fb4d", "73431a9b10"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mut_freqs": [0.0079155672823219, 0.010554089709762533, 0.0158311345646438, 0.018469656992084433, 0.013192612137203167, 0.010554089709762533, 0.013192612137203167], "n_mutations": [3, 4, 6, 7, 5, 4, 5], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, true, true, true, false, false], "loci": ["igh", "igh", "igh", "igh", "igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 345}}, {"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["16df39683f", "7f6d2ba874", "6e208eca11"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mut_freqs": [0.0158311345646438, 0.010554089709762533, 0.023746701846965697], "n_mutations": [6, 4, 9], "input_seqs": ["NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTAAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGGGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGATCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATGTTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAAGGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCTAGAGACTGCGAAGCAGCTGGTACCTGTTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGACAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV3-7*05": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999030671394, "IGHD6-19*01": 9.69328761020389e-08}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, true], "loci": ["igh", "igh", "igh"], "codon_positions": {"v": 288, "j": 348}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["226be79d5f", "188e1a0235"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD3-16*02": 1.0}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 288, "j": 339}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["93c01dd961", "c761732a8b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mut_freqs": [0.002840909090909091, 0.005681818181818182], "n_mutations": [1, 2], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACAAGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD1-20*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "TCTCAGA", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "loci": ["igh", "igh"], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["e64fcd9e03"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.01098901098901099], "n_mutations": [4], "input_seqs": ["NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGGGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTCTCCTGGTGACTCTGATGCCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGACTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV5-51*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9816252828850575, "IGHD6-13*01": 0.018374717114945146}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["401a542698"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mut_freqs": [0.013850415512465374], "n_mutations": [5], "input_seqs": ["NNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTACTTACTACTGGAGCTGGATCCGGCAGTCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCAAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGTAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*09": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999996029153599, "IGHD6-19*01": 3.9708463321213133e-07}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [true], "qr_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACC............AGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["d8761c689a"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 64, "mut_freqs": [0.020887728459530026], "n_mutations": [8], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GAATACT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 349}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["adc41b4237"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mut_freqs": [0.013513513513513514], "n_mutations": [5], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTGCATGAGCTGGGTCCGCCAGGCTCCACGGGAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAAGACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999913297444, "IGHD6-19*01": 8.670260428895021e-09}, "j_per_gene_support": {"IGHJ4*02": 1.0}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAGGA", "dj_insertion": "GGCGCCC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "loci": ["igh"], "codon_positions": {"v": 288, "j": 342}}]}

test/paired/new-results/partition-new-simu/fasttree/iclust-0/log CHANGED Viewed

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.06
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07 (final)
-Optimize all lengths: LogLk = -1661.140 Time 0.07
-Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
+Optimize all lengths: LogLk = -1661.140 Time 0.08
+Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-1/log CHANGED Viewed

@@ -9,15 +9,15 @@ Ignored unknown character X (seen 176 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
 Total branch-length 0.116 after 0.01 sec
-ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.01
+ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.02
 GTR Frequencies: 0.2498 0.2482 0.2788 0.2231
 GTR rates(ac ag at cg ct gt) 0.7186 0.4400 0.9760 0.8085 0.8107 1.0000
 Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.652 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.07
+ML-NNI round 2: LogLk = -1478.013 NNIs 0 max delta 0.00 Time 0.06
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.08 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.09
-Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.07 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.07
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-2/log CHANGED Viewed

@@ -19,5 +19,5 @@ Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.05
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.06 (final)
-Optimize all lengths: LogLk = -1274.921 Time 0.06
+Optimize all lengths: LogLk = -1274.921 Time 0.07
 Total time: 0.07 seconds Unique: 6/6 Bad splits: 0/3

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log CHANGED Viewed

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -968.466 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -968.442 NNIs 0 max delta 0.00 Time 0.03 (final)
+ML-NNI round 3: LogLk = -968.442 NNIs 0 max delta 0.00 Time 0.04 (final)
 Optimize all lengths: LogLk = -968.442 Time 0.04
 Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log CHANGED Viewed

@@ -16,7 +16,7 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.658 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.03 (final)
 Optimize all lengths: LogLk = -794.513 Time 0.03