partis-bcr 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12__cp312-cp312-macosx_10_13_universal2.whl

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Files changed (49) hide show
  1. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/RECORD +49 -49
  3. test/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  4. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  5. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  6. test/new-results/run-times.csv +8 -8
  7. test/new-results/test.log +46 -46
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +6 -6
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  12. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +1 -1
  13. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +2 -2
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  29. test/paired/new-results/run-times.csv +6 -6
  30. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +47 -43
  31. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +56 -52
  32. test/paired/new-results/subset-partition-new-simu/merged-partition.log +28 -24
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  34. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  36. test/paired/new-results/test.log +127 -118
  37. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/cf-alleles.py +0 -0
  38. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/cf-germlines.py +0 -0
  39. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/compare-plotdirs.py +0 -0
  40. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/extract-pairing-info.py +0 -0
  41. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/gctree-run.py +0 -0
  42. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/get-naive-probabilities.py +0 -0
  43. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/parse-output.py +0 -0
  44. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/partis-test.py +0 -0
  45. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/split-loci.py +0 -0
  46. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/WHEEL +0 -0
  47. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/entry_points.txt +0 -0
  48. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/licenses/COPYING +0 -0
  49. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/top_level.txt +0 -0
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test/paired/new-results/run-times.csv CHANGED
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  name,seconds
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- cache-parameters-simu,31.6
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- partition-new-simu,37.9
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- subset-partition-new-simu,123.2
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- seed-partition-new-simu,21.1
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- get-selection-metrics-new-simu,11.2
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- cache-parameters-data,37.0
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+ cache-parameters-simu,34.9
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+ partition-new-simu,36.9
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+ subset-partition-new-simu,135.7
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+ seed-partition-new-simu,19.8
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
@@ -36,7 +36,7 @@ writing to paired subdirs
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  run partis cache-parameters --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
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  --input-metafnames: added meta info for 24 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
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  caching parameters
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- vsearch: 24 / 24 v annotations (0 failed) with 8 v genes in 0.2 sec
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+ vsearch: 24 / 24 v annotations (0 failed) with 8 v genes in 0.1 sec
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  keeping 6 / 198 v genes
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  vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
@@ -50,23 +50,23 @@ smith-waterman (writing parameters)
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  info for 24 / 24 = 1.000 (removed: 0 failed)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (1.2 sec)
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- water time: 1.5 (ig-sw 1.4 processing 0.2)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (1.0 sec)
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+ water time: 1.2 (ig-sw 1.1 processing 0.2)
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  writing hmms removed 21 genes from glfo (leaving v 6 d 13 j 4)
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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- (0.7 sec)
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+ (0.9 sec)
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  hmm
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.7 sec)
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- infra time: 0.8
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- hmm step time: 1.3
62
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (1.1 sec)
63
+ infra time: 1.2
64
+ hmm step time: 1.8
65
65
  writing hmms removed 4 genes from glfo (leaving v 6 d 9 j 4)
66
66
 
67
67
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
68
- (0.6 sec)
69
- total time: 4.9
68
+ (0.7 sec)
69
+ total time: 5.2
70
70
  cache-parameters igk:
71
71
  run partis cache-parameters --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
72
72
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -74,30 +74,30 @@ caching parameters
74
74
  vsearch: 18 / 18 v annotations (0 failed) with 6 v genes in 0.1 sec
75
75
  keeping 5 / 64 v genes
76
76
  smith-waterman (new-allele fitting)
77
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
77
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
78
78
  running 10 procs for 18 seqs
79
79
  running 11 procs for 2 seqs
80
80
  info for 18 / 18 = 1.000 (removed: 0 failed)
81
81
  kept 5 (0.278) unproductive
82
82
  water time: 0.3 (ig-sw 0.0 processing 0.1)
83
83
  smith-waterman (writing parameters)
84
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
84
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
85
85
  running 10 procs for 18 seqs
86
86
  running 11 procs for 2 seqs
87
87
  info for 18 / 18 = 1.000 (removed: 0 failed)
88
88
  kept 5 (0.278) unproductive
89
89
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
90
90
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (0.7 sec)
91
- water time: 1.1 (ig-sw 0.7 processing 0.1)
91
+ water time: 1.0 (ig-sw 0.7 processing 0.1)
92
92
  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
93
93
 
94
94
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
95
- (0.4 sec)
95
+ (0.5 sec)
96
96
  hmm
97
97
  reading output
98
98
  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
99
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.7 sec)
100
- infra time: 0.8
99
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.6 sec)
100
+ infra time: 0.7
101
101
  hmm step time: 1.1
102
102
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
103
103
 
@@ -111,19 +111,19 @@ caching parameters
111
111
  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
112
112
  keeping 3 / 80 v genes
113
113
  smith-waterman (new-allele fitting)
114
- vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.0 sec
114
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
115
115
  running 10 procs for 10 seqs
116
116
  info for 10 / 10 = 1.000 (removed: 0 failed)
117
117
  kept 7 (0.700) unproductive
118
- water time: 0.2 (ig-sw 0.0 processing 0.1)
118
+ water time: 0.1 (ig-sw 0.0 processing 0.1)
119
119
  smith-waterman (writing parameters)
120
- vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 sec
120
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
121
121
  running 10 procs for 10 seqs
122
122
  info for 10 / 10 = 1.000 (removed: 0 failed)
123
123
  kept 7 (0.700) unproductive
124
124
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
125
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw (0.4 sec)
126
- water time: 0.6 (ig-sw 0.5 processing 0.2)
125
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw (0.5 sec)
126
+ water time: 0.7 (ig-sw 0.6 processing 0.2)
127
127
  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
128
128
 
129
129
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -131,14 +131,14 @@ smith-waterman (writing parameters)
131
131
  hmm
132
132
  reading output
133
133
  read 10 hmm output lines with 10 sequences in 10 events (0 failures)
134
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.3 sec)
135
- infra time: 0.4
136
- hmm step time: 0.7
134
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.5 sec)
135
+ infra time: 0.5
136
+ hmm step time: 0.8
137
137
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
138
138
 
139
139
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
140
140
  (0.2 sec)
141
- total time: 2.3
141
+ total time: 2.6
142
142
  partition igh:
143
143
  run partis partition --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
144
144
  --input-metafnames: added meta info for 24 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -150,26 +150,26 @@ smith-waterman
150
150
  kept 11 (0.458) unproductive
151
151
  water time: 0.0
152
152
  hmm
153
- caching all 24 naive sequences (0.5s)
153
+ caching all 24 naive sequences (0.6s)
154
154
  collapsed 24 queries into 22 clusters with identical naive seqs (0.0 sec)
155
155
  22 clusters with 10 procs (0.4s)
156
156
  22 clusters with 7 procs (0.4s)
157
157
  20 clusters with 5 procs (0.4s)
158
- 18 clusters with 3 procs (0.4s)
158
+ 18 clusters with 3 procs (0.5s)
159
159
  14 clusters with 2 procs (0.4s)
160
- 12 clusters with 1 proc (0.3s)
160
+ 12 clusters with 1 proc (0.4s)
161
161
  note not merging entire cpath history
162
- partition loop time: 2.3
162
+ partition loop time: 2.4
163
163
  getting annotations for final partition
164
- subcluster annotating 12 clusters with steps: (0.5s) (0.2s)
164
+ subcluster annotating 12 clusters with steps: (0.5s) (0.3s)
165
165
  subcluster annotation time 0.7
166
- total time: 3.7
166
+ total time: 3.9
167
167
  partition igk:
168
168
  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
169
169
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
170
170
  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm)
171
171
  smith-waterman
172
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
172
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
173
173
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
174
174
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
175
175
  kept 5 (0.278) unproductive
@@ -182,12 +182,12 @@ hmm
182
182
  7 clusters with 5 procs (0.3s)
183
183
  7 clusters with 3 procs (0.2s)
184
184
  7 clusters with 2 procs (0.2s)
185
- 7 clusters with 1 proc (0.3s)
185
+ 7 clusters with 1 proc (0.4s)
186
186
  partition loop time: 1.3
187
187
  getting annotations for final partition
188
188
  subcluster annotating 6 clusters with steps: (0.3s) (0.2s)
189
189
  subcluster annotation time 0.5
190
- total time: 2.3
190
+ total time: 2.4
191
191
  partition igl:
192
192
  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
193
193
  --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -204,8 +204,8 @@ hmm
204
204
  reducing n procs to number of clusters: 10 --> 3
205
205
  3 clusters with 3 procs (0.2s)
206
206
  3 clusters with 2 procs (0.2s)
207
- 3 clusters with 1 proc (0.3s)
208
- partition loop time: 0.7
207
+ 3 clusters with 1 proc (0.2s)
208
+ partition loop time: 0.6
209
209
  getting annotations for final partition
210
210
  subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
211
211
  subcluster annotation time 0.4
@@ -229,6 +229,7 @@ cleaning pair info for 52 seqs
229
229
  k 0 0 3
230
230
  merge time 0.0
231
231
  need to get annotations for 1/8 joint igh clusters
232
+ tag: v1.0.12
232
233
  annotate igh+igk: igh
233
234
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh-only-partition.yaml
234
235
  --input-metafnames: added meta info for 16 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml: loci paired-uids
@@ -241,23 +242,24 @@ smith-waterman
241
242
  kept 6 (0.375) unproductive
242
243
  water time: 0.0
243
244
  hmm
244
- subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
245
- subcluster annotation time 0.6
246
- total time: 0.8
245
+ subcluster annotating 8 clusters with steps: (0.6s) (0.3s)
246
+ subcluster annotation time 0.9
247
+ total time: 1.1
247
248
  need to get annotations for 5/8 joint igk clusters
249
+ tag: v1.0.12
248
250
  annotate igh+igk: igk
249
251
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
250
252
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml: loci paired-uids
251
253
  --input-partition-fname: read best partition with 18 sequences in 8 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
252
254
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm)
253
255
  smith-waterman
254
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
256
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
255
257
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
256
258
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
257
259
  kept 5 (0.278) unproductive
258
260
  water time: 0.0
259
261
  hmm
260
- subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
262
+ subcluster annotating 8 clusters with steps: (0.3s) (0.2s)
261
263
  subcluster annotation time 0.5
262
264
  total time: 0.7
263
265
  igh+igl: synchronizing heavy and light chain cluster paths
@@ -275,6 +277,7 @@ hmm
275
277
  h 0 0 0
276
278
  l 0 0 0
277
279
  merge time 0.0
280
+ tag: v1.0.12
278
281
  annotate igh+igl: igh
279
282
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh-only-partition.yaml
280
283
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml: loci paired-uids
@@ -292,6 +295,7 @@ hmm
292
295
  subcluster annotation time 0.4
293
296
  total time: 0.5
294
297
  need to get annotations for 2/3 joint igl clusters
298
+ tag: v1.0.12
295
299
  annotate igh+igl: igl
296
300
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl-only-partition.yaml
297
301
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml: loci paired-uids
@@ -305,8 +309,8 @@ smith-waterman
305
309
  kept 6 (0.857) unproductive
306
310
  water time: 0.0
307
311
  hmm
308
- subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
309
- subcluster annotation time 0.3
312
+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
313
+ subcluster annotation time 0.4
310
314
  total time: 0.5
311
315
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml
312
316
  concatenating heavy chain loci:
@@ -320,4 +324,4 @@ hmm
320
324
  h 12 --> 11 -1
321
325
  k 6 --> 8 +2
322
326
  l 3 --> 3
323
- total time: 43.0
327
+ total time: 47.3