partis-bcr 1.0.12__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (49) hide show
  1. packages/bpp/bin/bppseqgen +0 -0
  2. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/METADATA +1 -1
  3. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/RECORD +49 -48
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  5. test/new-results/run-times.csv +8 -8
  6. test/new-results/test.log +43 -43
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +6 -6
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +6 -6
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  10. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/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 -51
  31. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +51 -55
  32. test/paired/new-results/subset-partition-new-simu/merged-partition.log +30 -34
  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 +129 -138
  37. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  38. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  39. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  40. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  41. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/gctree-run.py +0 -0
  42. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  43. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/parse-output.py +0 -0
  44. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/partis-test.py +0 -0
  45. {partis_bcr-1.0.12.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/split-loci.py +0 -0
  46. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/WHEEL +0 -0
  47. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/entry_points.txt +0 -0
  48. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/licenses/COPYING +0 -0
  49. {partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev3.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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3
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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  kept 11 (0.458) unproductive
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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 parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (0.8 sec)
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+ water time: 1.1 (ig-sw 0.9 processing 0.2)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (1.1 sec)
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- infra time: 1.2
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- hmm step time: 1.8
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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
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+ total time: 4.2
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71
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  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
@@ -79,7 +79,7 @@ smith-waterman (new-allele fitting)
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
- water time: 0.3 (ig-sw 0.0 processing 0.1)
82
+ water time: 0.3 (ig-sw 0.0 processing 0.2)
83
83
  smith-waterman (writing parameters)
84
84
  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
85
85
  running 10 procs for 18 seqs
@@ -87,23 +87,23 @@ smith-waterman (writing parameters)
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
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (0.7 sec)
91
- water time: 1.0 (ig-sw 0.7 processing 0.1)
90
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (0.6 sec)
91
+ water time: 1.0 (ig-sw 0.7 processing 0.2)
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
- (0.5 sec)
95
+ (0.4 sec)
96
96
  hmm
97
97
  reading output
98
98
  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
99
99
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.6 sec)
100
100
  infra time: 0.7
101
- hmm step time: 1.1
101
+ hmm step time: 1.0
102
102
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
103
103
 
104
104
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
105
105
  (0.4 sec)
106
- total time: 3.8
106
+ total time: 3.7
107
107
  cache-parameters igl:
108
108
  run partis cache-parameters --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 --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
109
109
  --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -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 0.1 sec
114
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 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: 0.1 (ig-sw 0.0 processing 0.1)
118
+ water time: 0.2 (ig-sw 0.0 processing 0.1)
119
119
  smith-waterman (writing parameters)
120
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 (0.5 sec)
126
- water time: 0.7 (ig-sw 0.6 processing 0.2)
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)
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 (0.5 sec)
135
- infra time: 0.5
136
- hmm step time: 0.8
134
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.4 sec)
135
+ infra time: 0.4
136
+ hmm step time: 0.7
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: 2.6
141
+ total time: 2.4
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
@@ -150,44 +150,44 @@ smith-waterman
150
150
  kept 11 (0.458) unproductive
151
151
  water time: 0.0
152
152
  hmm
153
- caching all 24 naive sequences (0.6s)
153
+ caching all 24 naive sequences (0.5s)
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 (0.5s)
158
+ 18 clusters with 3 procs (0.4s)
159
159
  14 clusters with 2 procs (0.4s)
160
- 12 clusters with 1 proc (0.4s)
160
+ 12 clusters with 1 proc (0.3s)
161
161
  note not merging entire cpath history
162
- partition loop time: 2.4
162
+ partition loop time: 2.3
163
163
  getting annotations for final partition
164
- subcluster annotating 12 clusters with steps: (0.5s) (0.3s)
164
+ subcluster annotating 12 clusters with steps: (0.5s) (0.2s)
165
165
  subcluster annotation time 0.7
166
- total time: 3.9
166
+ total time: 3.6
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 0.2 sec
172
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 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
176
176
  water time: 0.0
177
177
  hmm
178
- caching all 18 naive sequences (0.4s)
178
+ caching all 18 naive sequences (0.3s)
179
179
  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
180
180
  reducing n procs to number of clusters: 10 --> 7
181
181
  7 clusters with 7 procs (0.3s)
182
- 7 clusters with 5 procs (0.3s)
182
+ 7 clusters with 5 procs (0.2s)
183
183
  7 clusters with 3 procs (0.2s)
184
184
  7 clusters with 2 procs (0.2s)
185
- 7 clusters with 1 proc (0.4s)
186
- partition loop time: 1.3
185
+ 7 clusters with 1 proc (0.3s)
186
+ partition loop time: 1.2
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: 2.4
190
+ total time: 2.2
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
@@ -208,8 +208,8 @@ hmm
208
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
- subcluster annotation time 0.4
212
- total time: 1.5
211
+ subcluster annotation time 0.3
212
+ total time: 1.4
213
213
  combining chains
214
214
  cleaning pair info for 52 seqs
215
215
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -229,31 +229,29 @@ 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
233
232
  annotate igh+igk: igh
234
233
  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
235
234
  --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
236
235
  --input-partition-fname: read best partition with 16 sequences in 8 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh-only-partition.yaml
237
236
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm)
238
237
  smith-waterman
239
- vsearch: 16 / 16 v annotations (0 failed) with 5 v genes in 0.2 sec
238
+ vsearch: 16 / 16 v annotations (0 failed) with 5 v genes in 0.1 sec
240
239
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
241
240
  info for 16 / 16 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
242
241
  kept 6 (0.375) unproductive
243
242
  water time: 0.0
244
243
  hmm
245
- subcluster annotating 8 clusters with steps: (0.6s) (0.3s)
246
- subcluster annotation time 0.9
247
- total time: 1.1
244
+ subcluster annotating 8 clusters with steps: (0.3s) (0.2s)
245
+ subcluster annotation time 0.5
246
+ total time: 0.6
248
247
  need to get annotations for 5/8 joint igk clusters
249
- tag: v1.0.12
250
248
  annotate igh+igk: igk
251
249
  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
252
250
  --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
253
251
  --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
254
252
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm)
255
253
  smith-waterman
256
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
254
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
257
255
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
258
256
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
259
257
  kept 5 (0.278) unproductive
@@ -277,7 +275,6 @@ hmm
277
275
  h 0 0 0
278
276
  l 0 0 0
279
277
  merge time 0.0
280
- tag: v1.0.12
281
278
  annotate igh+igl: igh
282
279
  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
283
280
  --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
@@ -285,7 +282,7 @@ hmm
285
282
  --input-partition-fname: read best partition with 7 sequences in 3 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh-only-partition.yaml
286
283
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm)
287
284
  smith-waterman
288
- vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.1 sec
285
+ vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.2 sec
289
286
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
290
287
  info for 7 / 7 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
291
288
  kept 4 (0.571) unproductive
@@ -293,9 +290,8 @@ smith-waterman
293
290
  hmm
294
291
  subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
295
292
  subcluster annotation time 0.4
296
- total time: 0.5
293
+ total time: 0.6
297
294
  need to get annotations for 2/3 joint igl clusters
298
- tag: v1.0.12
299
295
  annotate igh+igl: igl
300
296
  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
301
297
  --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
@@ -303,13 +299,13 @@ hmm
303
299
  --input-partition-fname: read best partition with 7 sequences in 3 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl-only-partition.yaml
304
300
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm)
305
301
  smith-waterman
306
- vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.2 sec
302
+ vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.1 sec
307
303
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
308
304
  info for 7 / 7 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
309
305
  kept 6 (0.857) unproductive
310
306
  water time: 0.0
311
307
  hmm
312
- subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
308
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
313
309
  subcluster annotation time 0.4
314
310
  total time: 0.5
315
311
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml
@@ -324,4 +320,4 @@ hmm
324
320
  h 12 --> 11 -1
325
321
  k 6 --> 8 +2
326
322
  l 3 --> 3
327
- total time: 47.3
323
+ total time: 39.9