partis-bcr 1.0.11__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl

test/new-results/test.log

@@ -1,34 +1,213 @@
-cache-parameters-quick-new-simu   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
+cache-parameters-simu            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 0.2 sec
-    keeping 2 / 198 v genes
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
+    keeping 7 / 198 v genes
+    missing 8 simulation genes (counts): hv1-202 0  hv2-502 0  hv2-70D04 0  hv3-1104 0  hv3-69-102 0  hv3-902 0  hv4-3401 0  hv4-3909 0
 smith-waterman  (new-allele fitting)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.1 sec
-    running 10 procs for 10 seqs
-      info for 10 / 10 = 1.000   (removed: 0 failed)
-      kept 10 (1.000) unproductive
-    water time: 0.2  (ig-sw 0.0  processing 0.2)
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 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: 0.4  (ig-sw 0.0  processing 0.1)
 smith-waterman  (writing parameters)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.2 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 0.2 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 (2.6 sec)
-    water time: 2.9  (ig-sw 2.7  processing 0.2)
-  writing hmms     removed 35 genes from glfo (leaving v 2  d 1  j 2)
+    writing parameters to test/new-results/test/parameters/simu/sw (1.3 sec)
+    water time: 1.8  (ig-sw 1.4  processing 0.2)
+  writing hmms     removed 30 genes from glfo (leaving v 7  d 5  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.2 sec)
+(0.7 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 (0.3 sec)
-         infra time: 0.4
+        read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
+    writing parameters to test/new-results/test/parameters/simu/hmm (1.1 sec)
+    writing parameters to test/new-results/test/parameters/simu/true (2.2 sec)
+         infra time: 3.5
+      hmm step time: 4.1
+  writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
+
+  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
+(0.7 sec)
+      total time: 8.3
+annotate-new-simu                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 0.1 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 
+    warning 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 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+         infra time: 0.1
       hmm step time: 0.8
-  writing hmms     removed 0  genes from glfo (leaving v 2  d 1  j 2)
+      total time: 1.1
+multi-annotate-new-simu          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 0.1 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 
+    warning 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
+  warning split apart 1 cluster that contained multiple cdr3 lengths (total clusters: 10 --> 11)
+      cluster splits:   8 --> 7 1
+  subcluster annotating 11 clusters with steps:  (0.6s) (0.2s)   plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+
+    subcluster annotation time 0.9
+      total time: 1.1
+partition-new-simu               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 0.1 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 
+    warning 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 (0.8s)
+    collapsed 36 queries into 12 clusters with identical naive seqs (0.0 sec)
+  12 clusters with 10 procs (0.3s)
+   12 clusters with 7 procs (0.3s)
+   12 clusters with 5 procs (0.2s)
+   12 clusters with 3 procs (0.2s)
+   12 clusters with 2 procs (0.3s)
+   11 clusters with 1 proc (0.5s)
+       partition loop time: 1.9
+getting annotations for final partition
+  subcluster annotating 10 clusters with steps:  (0.6s) (0.2s) (0.2s)   plotting performance 
+    warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
+(0.0 sec)
+
+    subcluster annotation time 1.1
+      total time: 4.1
+seed-partition-new-simu          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 0.1 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 (0.1s)
+       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 (0.2s)
+       partition loop time: 0.3
+getting annotations for final partition
+  subcluster annotating 1 cluster with steps:  (0.3s) (0.2s) (0.1s) 
+    subcluster annotation time 0.6
+  seed cluster size in best partition: 11, excluding seed seq: 10
+      total time: 1.2
+vsearch-partition-new-simu       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 0.2 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: 0.3
+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:  (0.5s) (0.2s) (0.2s) 
+    subcluster annotation time 0.9
+      total time: 1.6
+get-selection-metrics-new-simu   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
+        run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
+        run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
+        run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
+      made 3 fasttree trees (0.7s)
+    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
+      warning 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 ikm psx
+      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
+      warning 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
+      warning 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 eyz fnv nox
+    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: 0.9
+cache-parameters-data            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 0.1 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: 0.3  (ig-sw 0.0  processing 0.1)
+smith-waterman  (writing parameters)
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.1 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 (1.4 sec)
+    water time: 1.9  (ig-sw 1.5  processing 0.1)
+  writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
+
+  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
+(2.2 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 (1.7 sec)
+         infra time: 1.9
+      hmm step time: 3.8
+  writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.3 sec)
-      total time: 4.9
+(2.1 sec)
+      total time: 10.7

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

@@ -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

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 32 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
-Total branch-length 0.172 after 0.01 sec
+Total branch-length 0.172 after 0.00 sec
 ML-NNI round 1: LogLk = -1718.230 NNIs 0 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2101 0.3021 0.2760 0.2118
 GTR rates(ac ag at cg ct gt) 1.2927 1.2254 1.4006 0.7465 1.0327 1.0000

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

@@ -19,5 +19,5 @@ Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -794.353 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.02 (final)
-Optimize all lengths: LogLk = -794.321 Time 0.03
+Optimize all lengths: LogLk = -794.321 Time 0.02
 Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4

test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
 Total branch-length 0.074 after 0.00 sec
-ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.01
+ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.00
 GTR Frequencies: 0.2044 0.3132 0.2728 0.2096
 GTR rates(ac ag at cg ct gt) 0.8954 1.2357 1.0576 0.3959 0.3435 1.0000
 Switched to using 20 rate categories (CAT approximation)