partis-bcr 1.0.13__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13.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 (53) hide show
  1. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/RECORD +53 -53
  3. python/processargs.py +4 -1
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  5. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  6. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  7. test/new-results/run-times.csv +8 -8
  8. test/new-results/test.log +53 -54
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +3 -3
  13. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +4 -4
  14. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +1 -1
  15. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +1 -1
  16. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +4 -4
  17. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +5 -5
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +108 -108
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +84 -84
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +62 -62
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +19 -19
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +25 -25
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +36 -36
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +23 -23
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +46 -46
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +46 -46
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +46 -46
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +16 -16
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +16 -16
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +48 -48
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +49 -49
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +28 -28
  33. test/paired/new-results/run-times.csv +6 -6
  34. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +64 -68
  35. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +64 -69
  36. test/paired/new-results/subset-partition-new-simu/merged-partition.log +44 -48
  37. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  38. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  39. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  40. test/paired/new-results/test.log +163 -172
  41. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  42. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  43. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  44. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  45. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/gctree-run.py +0 -0
  46. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  47. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/parse-output.py +0 -0
  48. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/partis-test.py +0 -0
  49. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev3.data}/scripts/split-loci.py +0 -0
  50. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/WHEEL +0 -0
  51. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/entry_points.txt +0 -0
  52. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev3.dist-info}/licenses/COPYING +0 -0
  53. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.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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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (1.1 sec)
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- water time: 1.4 (ig-sw 1.2 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: 1.0 (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 (1.3 sec)
63
- infra time: 1.4
64
- hmm step time: 2.0
62
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.7 sec)
63
+ infra time: 0.8
64
+ hmm step time: 1.3
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
- (1.0 sec)
69
- total time: 6.0
68
+ (0.6 sec)
69
+ total time: 4.2
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
@@ -74,36 +74,36 @@ 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 0.2 sec
77
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 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
- water time: 0.3 (ig-sw 0.0 processing 0.2)
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 0.1 sec
84
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 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
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (1.2 sec)
91
- water time: 1.6 (ig-sw 1.3 processing 0.2)
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)
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
- (0.7 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
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (1.2 sec)
100
- infra time: 1.3
101
- hmm step time: 1.8
99
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.7 sec)
100
+ infra time: 0.9
101
+ hmm step time: 1.2
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
- (0.6 sec)
106
- total time: 5.5
105
+ (0.5 sec)
106
+ total time: 3.8
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
@@ -115,30 +115,30 @@ smith-waterman (new-allele fitting)
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 0.2)
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 0.1 sec
120
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 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 (1.1 sec)
126
- water time: 1.3 (ig-sw 1.2 processing 0.1)
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 0.1)
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
130
- (0.5 sec)
130
+ (0.3 sec)
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 (0.6 sec)
135
- infra time: 0.7
136
- hmm step time: 1.2
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
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
- (0.4 sec)
141
- total time: 3.9
140
+ (0.2 sec)
141
+ total time: 2.2
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
@@ -150,20 +150,20 @@ smith-waterman
150
150
  kept 11 (0.458) unproductive
151
151
  water time: 0.0
152
152
  hmm
153
- caching all 24 naive sequences (0.9s)
153
+ caching all 24 naive sequences (0.5s)
154
154
  collapsed 24 queries into 22 clusters with identical naive seqs (0.0 sec)
155
- 22 clusters with 10 procs (0.5s)
156
- 22 clusters with 7 procs (0.4s)
157
- 20 clusters with 5 procs (0.4s)
155
+ 22 clusters with 10 procs (0.4s)
156
+ 22 clusters with 7 procs (0.3s)
157
+ 20 clusters with 5 procs (0.3s)
158
158
  18 clusters with 3 procs (0.5s)
159
- 14 clusters with 2 procs (0.5s)
160
- 12 clusters with 1 proc (0.5s)
159
+ 14 clusters with 2 procs (0.4s)
160
+ 12 clusters with 1 proc (0.3s)
161
161
  note not merging entire cpath history
162
- partition loop time: 2.8
162
+ partition loop time: 2.1
163
163
  getting annotations for final partition
164
- subcluster annotating 12 clusters with steps: (0.7s) (0.3s)
165
- subcluster annotation time 0.9
166
- total time: 4.9
164
+ subcluster annotating 12 clusters with steps: (0.4s) (0.2s)
165
+ subcluster annotation time 0.6
166
+ total time: 3.5
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
@@ -175,41 +175,41 @@ smith-waterman
175
175
  kept 5 (0.278) unproductive
176
176
  water time: 0.0
177
177
  hmm
178
- caching all 18 naive sequences (0.5s)
178
+ caching all 18 naive sequences (0.4s)
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
- 7 clusters with 7 procs (0.2s)
182
- 7 clusters with 5 procs (0.3s)
181
+ 7 clusters with 7 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: 1.4
185
+ 7 clusters with 1 proc (0.3s)
186
+ partition loop time: 1.3
187
187
  getting annotations for final partition
188
- subcluster annotating 6 clusters with steps: (0.4s) (0.2s)
189
- subcluster annotation time 0.6
190
- total time: 2.8
188
+ subcluster annotating 6 clusters with steps: (0.3s) (0.2s)
189
+ subcluster annotation time 0.5
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
194
194
  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm)
195
195
  smith-waterman
196
- vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 sec
196
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
197
197
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
198
198
  info for 10 / 10 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
199
199
  kept 7 (0.700) unproductive
200
200
  water time: 0.0
201
201
  hmm
202
- caching all 10 naive sequences (0.5s)
202
+ caching all 10 naive sequences (0.3s)
203
203
  collapsed 10 queries into 3 clusters with identical naive seqs (0.0 sec)
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
- subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
210
+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
211
211
  subcluster annotation time 0.4
212
- total time: 1.9
212
+ total time: 1.3
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
@@ -229,7 +229,6 @@ 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: v1.0.13
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
@@ -242,11 +241,10 @@ smith-waterman
242
241
  kept 6 (0.375) unproductive
243
242
  water time: 0.0
244
243
  hmm
245
- subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
246
- subcluster annotation time 0.7
247
- total time: 0.9
244
+ subcluster annotating 8 clusters with steps: (0.4s) (0.1s)
245
+ subcluster annotation time 0.5
246
+ total time: 0.7
248
247
  need to get annotations for 5/8 joint igk clusters
249
- tag: v1.0.13
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
@@ -261,7 +259,7 @@ smith-waterman
261
259
  hmm
262
260
  subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
263
261
  subcluster annotation time 0.6
264
- total time: 0.8
262
+ total time: 0.7
265
263
  igh+igl: synchronizing heavy and light chain cluster paths
266
264
  removing badly + unpaired seqs: kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0 l 0
267
265
  note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -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: v1.0.13
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
@@ -291,11 +288,10 @@ smith-waterman
291
288
  kept 4 (0.571) unproductive
292
289
  water time: 0.0
293
290
  hmm
294
- subcluster annotating 3 clusters with steps: (0.2s) (0.3s)
291
+ subcluster annotating 3 clusters with steps: (0.3s) (0.2s)
295
292
  subcluster annotation time 0.5
296
293
  total time: 0.6
297
294
  need to get annotations for 2/3 joint igl clusters
298
- tag: v1.0.13
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
@@ -303,15 +299,15 @@ 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: (0.3s) (0.2s)
313
- subcluster annotation time 0.5
314
- total time: 0.7
308
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
309
+ subcluster annotation time 0.4
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
316
312
  concatenating heavy chain loci:
317
313
  h starting with 8 annotations (16 seqs)
@@ -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: 62.9
323
+ total time: 41.2