partis-bcr 1.0.12.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13__cp312-cp312-macosx_10_13_universal2.whl

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Files changed (50) hide show
  1. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/RECORD +50 -50
  3. test/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  4. test/new-results/partition-new-simu/fasttree/iclust-2/log +3 -3
  5. test/new-results/run-times.csv +7 -7
  6. test/new-results/test.log +43 -43
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  10. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +3 -3
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +2 -2
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +1 -1
  13. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +1 -1
  14. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +4 -4
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  30. test/paired/new-results/run-times.csv +6 -6
  31. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +66 -62
  32. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +48 -44
  33. test/paired/new-results/subset-partition-new-simu/merged-partition.log +38 -34
  34. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  36. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  37. test/paired/new-results/test.log +140 -131
  38. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/cf-alleles.py +0 -0
  39. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/cf-germlines.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/compare-plotdirs.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/extract-pairing-info.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/gctree-run.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/get-naive-probabilities.py +0 -0
  44. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/parse-output.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/partis-test.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/split-loci.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/WHEEL +0 -0
  48. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/entry_points.txt +0 -0
  49. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/licenses/COPYING +0 -0
  50. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.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,34.7
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- partition-new-simu,42.0
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- subset-partition-new-simu,155.0
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- seed-partition-new-simu,22.6
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+ subset-partition-new-simu,180.3
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
@@ -39,34 +39,34 @@ caching parameters
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  vsearch: 24 / 24 v annotations (0 failed) with 8 v genes in 0.1 sec
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- vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
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+ vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.2 sec
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  running 10 procs for 24 seqs
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  info for 24 / 24 = 1.000 (removed: 0 failed)
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  kept 11 (0.458) unproductive
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+ water time: 0.2 (ig-sw 0.0 processing 0.2)
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  smith-waterman (writing parameters)
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- vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
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+ vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.2 sec
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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: 1.3 (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 (1.1 sec)
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+ water time: 1.4 (ig-sw 1.2 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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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (1.0 sec)
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- infra time: 1.1
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- hmm step time: 1.9
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (1.3 sec)
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+ infra time: 1.4
64
+ hmm step time: 2.0
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
- (0.8 sec)
69
- total time: 5.6
68
+ (1.0 sec)
69
+ total time: 6.0
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
@@ -74,12 +74,12 @@ 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 0.1 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
- 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 (1.4 sec)
91
- water time: 1.9 (ig-sw 1.5 processing 0.2)
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)
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
- (0.9 sec)
95
+ (0.7 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 (0.8 sec)
100
- infra time: 1.2
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
101
  hmm step time: 1.8
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
- (0.7 sec)
106
- total time: 6.1
105
+ (0.6 sec)
106
+ total time: 5.5
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
@@ -117,53 +117,53 @@ smith-waterman (new-allele fitting)
117
117
  kept 7 (0.700) unproductive
118
118
  water time: 0.2 (ig-sw 0.0 processing 0.2)
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 (0.5 sec)
126
- water time: 0.8 (ig-sw 0.6 processing 0.2)
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)
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
- (0.3 sec)
130
+ (0.5 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 (0.4 sec)
135
- infra time: 0.6
136
- hmm step time: 1.0
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
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
- (0.3 sec)
141
- total time: 3.1
140
+ (0.4 sec)
141
+ total time: 3.9
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
145
145
  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm)
146
146
  smith-waterman
147
- vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
147
+ vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.2 sec
148
148
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
149
149
  info for 24 / 24 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
150
150
  kept 11 (0.458) unproductive
151
151
  water time: 0.0
152
152
  hmm
153
- caching all 24 naive sequences (0.8s)
153
+ caching all 24 naive sequences (0.9s)
154
154
  collapsed 24 queries into 22 clusters with identical naive seqs (0.0 sec)
155
155
  22 clusters with 10 procs (0.5s)
156
- 22 clusters with 7 procs (0.8s)
157
- 20 clusters with 5 procs (0.5s)
156
+ 22 clusters with 7 procs (0.4s)
157
+ 20 clusters with 5 procs (0.4s)
158
158
  18 clusters with 3 procs (0.5s)
159
- 14 clusters with 2 procs (0.4s)
160
- 12 clusters with 1 proc (0.4s)
159
+ 14 clusters with 2 procs (0.5s)
160
+ 12 clusters with 1 proc (0.5s)
161
161
  note not merging entire cpath history
162
- partition loop time: 3.3
162
+ partition loop time: 2.8
163
163
  getting annotations for final partition
164
- subcluster annotating 12 clusters with steps: (0.6s) (0.3s)
164
+ subcluster annotating 12 clusters with steps: (0.7s) (0.3s)
165
165
  subcluster annotation time 0.9
166
- total time: 5.1
166
+ total time: 4.9
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
@@ -178,38 +178,38 @@ hmm
178
178
  caching all 18 naive sequences (0.5s)
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 (0.3s)
181
+ 7 clusters with 7 procs (0.2s)
182
182
  7 clusters with 5 procs (0.3s)
183
183
  7 clusters with 3 procs (0.2s)
184
- 7 clusters with 2 procs (0.3s)
184
+ 7 clusters with 2 procs (0.2s)
185
185
  7 clusters with 1 proc (0.4s)
186
186
  partition loop time: 1.4
187
187
  getting annotations for final partition
188
- subcluster annotating 6 clusters with steps: (0.5s) (0.2s)
189
- subcluster annotation time 0.8
190
- total time: 2.9
188
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s)
189
+ subcluster annotation time 0.6
190
+ total time: 2.8
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 0.1 sec
196
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 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 (0.4s)
202
+ caching all 10 naive sequences (0.5s)
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
- 3 clusters with 3 procs (0.3s)
205
+ 3 clusters with 3 procs (0.2s)
206
206
  3 clusters with 2 procs (0.2s)
207
207
  3 clusters with 1 proc (0.3s)
208
208
  partition loop time: 0.7
209
209
  getting annotations for final partition
210
- subcluster annotating 3 clusters with steps: (0.3s) (0.2s)
211
- subcluster annotation time 0.5
212
- total time: 1.7
210
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
211
+ subcluster annotation time 0.4
212
+ total time: 1.9
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
@@ -229,37 +229,39 @@ 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
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
235
236
  --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
236
237
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm)
237
238
  smith-waterman
238
- vsearch: 16 / 16 v annotations (0 failed) with 5 v genes in 0.1 sec
239
+ vsearch: 16 / 16 v annotations (0 failed) with 5 v genes in 0.2 sec
239
240
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
240
241
  info for 16 / 16 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
241
242
  kept 6 (0.375) unproductive
242
243
  water time: 0.0
243
244
  hmm
244
245
  subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
245
- subcluster annotation time 0.6
246
- total time: 0.7
246
+ subcluster annotation time 0.7
247
+ total time: 0.9
247
248
  need to get annotations for 5/8 joint igk clusters
249
+ tag: v1.0.13
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 0.2 sec
256
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 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: (0.5s) (0.2s)
261
- subcluster annotation time 0.7
262
- total time: 0.9
262
+ subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
263
+ subcluster annotation time 0.6
264
+ total time: 0.8
263
265
  igh+igl: synchronizing heavy and light chain cluster paths
264
266
  removing badly + unpaired seqs: kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0 l 0
265
267
  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
@@ -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: v1.0.13
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
@@ -288,10 +291,11 @@ smith-waterman
288
291
  kept 4 (0.571) unproductive
289
292
  water time: 0.0
290
293
  hmm
291
- subcluster annotating 3 clusters with steps: (0.3s) (0.2s)
294
+ subcluster annotating 3 clusters with steps: (0.2s) (0.3s)
292
295
  subcluster annotation time 0.5
293
296
  total time: 0.6
294
297
  need to get annotations for 2/3 joint igl clusters
298
+ tag: v1.0.13
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
@@ -299,15 +303,15 @@ hmm
299
303
  --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
300
304
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm)
301
305
  smith-waterman
302
- vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.1 sec
306
+ vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.2 sec
303
307
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
304
308
  info for 7 / 7 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
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) (0.1s)
309
- subcluster annotation time 0.4
310
- total time: 0.5
312
+ subcluster annotating 3 clusters with steps: (0.3s) (0.2s)
313
+ subcluster annotation time 0.5
314
+ total time: 0.7
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:
313
317
  h starting with 8 annotations (16 seqs)
@@ -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: 53.7
327
+ total time: 62.9