partis-bcr 1.0.13__cp312-cp312-manylinux1_x86_64.whl → 1.0.13.post1.dev2__cp312-cp312-manylinux1_x86_64.whl

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Files changed (47) hide show
  1. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/RECORD +47 -47
  3. python/processargs.py +4 -1
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  5. test/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  6. test/new-results/run-times.csv +7 -7
  7. test/new-results/test.log +12 -12
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +108 -108
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +84 -84
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +62 -62
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +19 -19
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +25 -25
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +36 -36
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +23 -23
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +46 -46
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +46 -46
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +46 -46
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +16 -16
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +16 -16
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +48 -48
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +49 -49
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +28 -28
  27. test/paired/new-results/run-times.csv +7 -7
  28. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -10
  29. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +10 -14
  30. test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -8
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  34. test/paired/new-results/test.log +84 -93
  35. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/cf-alleles.py +0 -0
  36. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/cf-germlines.py +0 -0
  37. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/compare-plotdirs.py +0 -0
  38. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/extract-pairing-info.py +0 -0
  39. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/gctree-run.py +0 -0
  40. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/get-naive-probabilities.py +0 -0
  41. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/parse-output.py +0 -0
  42. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/partis-test.py +0 -0
  43. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/split-loci.py +0 -0
  44. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/WHEEL +0 -0
  45. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/entry_points.txt +0 -0
  46. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/licenses/COPYING +0 -0
  47. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.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,14.4
3
- partition-new-simu,22.9
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- subset-partition-new-simu,75.3
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- seed-partition-new-simu,11.4
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- get-selection-metrics-new-simu,7.5
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test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
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  read 24 hmm output lines with 24 sequences in 24 events (0 failures)
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  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.5 sec)
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+ hmm step time: 1.0
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+ total time: 2.9
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  cache-parameters igk:
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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
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  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -75,7 +75,7 @@ smith-waterman (new-allele fitting)
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  running 11 procs for 2 seqs
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  kept 5 (0.278) unproductive
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+ water time: 0.0 (ig-sw 0.0 processing 0.0)
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  smith-waterman (writing parameters)
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  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
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  22 clusters with 10 procs (0.1s)
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  22 clusters with 7 procs (0.2s)
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  20 clusters with 5 procs (0.2s)
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+ 18 clusters with 3 procs (0.2s)
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  14 clusters with 2 procs (0.2s)
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@@ -217,7 +217,6 @@ cleaning pair info for 52 seqs
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  k 0 0 3
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218
  merge time 0.0
219
219
  need to get annotations for 1/8 joint igh clusters
220
- tag: v1.0.13
221
220
  annotate igh+igk: igh
222
221
  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
223
222
  --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
@@ -234,7 +233,6 @@ hmm
234
233
  subcluster annotation time 0.3
235
234
  total time: 0.4
236
235
  need to get annotations for 5/8 joint igk clusters
237
- tag: v1.0.13
238
236
  annotate igh+igk: igk
239
237
  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
240
238
  --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
@@ -265,7 +263,6 @@ hmm
265
263
  h 0 0 0
266
264
  l 0 0 0
267
265
  merge time 0.0
268
- tag: v1.0.13
269
266
  annotate igh+igl: igh
270
267
  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
271
268
  --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
@@ -281,9 +278,8 @@ smith-waterman
281
278
  hmm
282
279
  subcluster annotating 3 clusters with steps: (0.1s) (0.1s)
283
280
  subcluster annotation time 0.2
284
- total time: 0.3
281
+ total time: 0.2
285
282
  need to get annotations for 2/3 joint igl clusters
286
- tag: v1.0.13
287
283
  annotate igh+igl: igl
288
284
  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
289
285
  --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
@@ -312,4 +308,4 @@ hmm
312
308
  h 12 --> 11 -1
313
309
  k 6 --> 8 +2
314
310
  l 3 --> 3
315
- total time: 25.9
311
+ total time: 24.5
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -43,7 +43,7 @@ smith-waterman (new-allele fitting)
43
43
  running 10 procs for 32 seqs
44
44
  info for 32 / 32 = 1.000 (removed: 0 failed)
45
45
  kept 14 (0.438) unproductive
46
- water time: 0.1 (ig-sw 0.0 processing 0.0)
46
+ water time: 0.0 (ig-sw 0.0 processing 0.0)
47
47
  smith-waterman (writing parameters)
48
48
  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.0 sec
49
49
  running 10 procs for 32 seqs
@@ -53,7 +53,7 @@ smith-waterman (writing parameters)
53
53
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.6 sec)
54
54
  water time: 0.7 (ig-sw 0.6 processing 0.0)
55
55
  writing hmms removed 18 genes from glfo (leaving v 6 d 16 j 4)
56
- (0.6 sec)
56
+ (0.5 sec)
57
57
  hmm
58
58
  reading output
59
59
  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
@@ -62,7 +62,7 @@ hmm
62
62
  hmm step time: 1.2
63
63
  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
64
64
  (0.5 sec)
65
- total time: 3.2
65
+ total time: 3.1
66
66
  cache-parameters igk:
67
67
  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-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
68
68
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -93,7 +93,7 @@ hmm
93
93
  hmm step time: 0.7
94
94
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
95
95
  (0.2 sec)
96
- total time: 1.9
96
+ total time: 1.8
97
97
  cache-parameters igl:
98
98
  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-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
99
99
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -136,20 +136,20 @@ smith-waterman
136
136
  kept 14 (0.438) unproductive
137
137
  water time: 0.0
138
138
  hmm
139
- caching all 32 naive sequences (0.7s)
139
+ caching all 32 naive sequences (0.6s)
140
140
  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
141
- 30 clusters with 10 procs (0.1s)
141
+ 30 clusters with 10 procs (0.2s)
142
142
  29 clusters with 7 procs (0.2s)
143
143
  28 clusters with 5 procs (0.3s)
144
144
  28 clusters with 3 procs (0.3s)
145
145
  23 clusters with 2 procs (0.3s)
146
146
  20 clusters with 1 proc (0.5s)
147
147
  note not merging entire cpath history
148
- partition loop time: 1.8
148
+ partition loop time: 1.7
149
149
  getting annotations for final partition
150
150
  subcluster annotating 16 clusters with steps: (0.5s) (0.1s)
151
151
  subcluster annotation time 0.6
152
- total time: 3.1
152
+ total time: 3.0
153
153
  partition igk:
154
154
  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-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
155
155
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -173,7 +173,7 @@ hmm
173
173
  getting annotations for final partition
174
174
  subcluster annotating 6 clusters with steps: (0.2s) (0.1s)
175
175
  subcluster annotation time 0.2
176
- total time: 1.0
176
+ total time: 0.9
177
177
  partition igl:
178
178
  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-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
179
179
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -215,7 +215,6 @@ cleaning pair info for 61 seqs
215
215
  k 0 0 1
216
216
  merge time 0.0
217
217
  need to get annotations for 2/11 joint igh clusters
218
- tag: v1.0.13
219
218
  annotate igh+igk: igh
220
219
  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-1/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
221
220
  --input-metafnames: added meta info for 19 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml: loci paired-uids
@@ -232,7 +231,6 @@ hmm
232
231
  subcluster annotation time 0.4
233
232
  total time: 0.5
234
233
  need to get annotations for 6/11 joint igk clusters
235
- tag: v1.0.13
236
234
  annotate igh+igk: igk
237
235
  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-1/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
238
236
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml: loci paired-uids
@@ -265,7 +263,6 @@ hmm
265
263
  l 0 0 1
266
264
  merge time 0.0
267
265
  need to get annotations for 2/5 joint igh clusters
268
- tag: v1.0.13
269
266
  annotate igh+igl: igh
270
267
  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-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
271
268
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -282,7 +279,6 @@ hmm
282
279
  subcluster annotation time 0.3
283
280
  total time: 0.4
284
281
  need to get annotations for 5/5 joint igl clusters
285
- tag: v1.0.13
286
282
  annotate igh+igl: igl
287
283
  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-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
288
284
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
@@ -310,4 +306,4 @@ hmm
310
306
  h 16 --> 16
311
307
  k 6 --> 11 +5
312
308
  l 3 --> 5 +2
313
- total time: 27.6
309
+ total time: 25.7
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -32,7 +32,7 @@ hmm
32
32
  23 clusters with 5 procs (0.3s)
33
33
  22 clusters with 3 procs (0.3s)
34
34
  21 clusters with 2 procs (0.1s)
35
- 21 clusters with 1 proc (0.5s)
35
+ 21 clusters with 1 proc (0.4s)
36
36
  partition loop time: 1.8
37
37
  getting annotations for final partition
38
38
  subcluster annotating 18 clusters with steps: (0.6s) (0.2s) (0.1s)
@@ -122,7 +122,7 @@ hmm
122
122
  partition loop time: 0.3
123
123
  getting annotations for final partition
124
124
  subcluster annotating 3 clusters with steps: (0.1s) (0.1s) (0.1s)
125
- subcluster annotation time 0.3
125
+ subcluster annotation time 0.2
126
126
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
127
127
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
128
128
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
@@ -165,7 +165,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
165
165
  joint 0.963 0.594
166
166
  merge time 0.0
167
167
  need to get annotations for 6/15 joint igh clusters
168
- tag: v1.0.13
169
168
  annotate igh+igk: igh
170
169
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
171
170
  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/igh+igk/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -179,11 +178,10 @@ smith-waterman
179
178
  kept 13 (0.371) unproductive
180
179
  water time: 0.0
181
180
  hmm
182
- subcluster annotating 15 clusters with steps: (0.5s) (0.1s)
181
+ subcluster annotating 15 clusters with steps: (0.4s) (0.1s)
183
182
  subcluster annotation time 0.6
184
183
  total time: 0.6
185
184
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.13
187
185
  annotate igh+igk: igk
188
186
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
189
187
  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/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -228,7 +226,6 @@ hmm
228
226
  joint 1.000 0.787
229
227
  merge time 0.0
230
228
  need to get annotations for 2/6 joint igh clusters
231
- tag: v1.0.13
232
229
  annotate igh+igl: igh
233
230
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
234
231
  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/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -246,7 +243,6 @@ hmm
246
243
  subcluster annotation time 0.5
247
244
  total time: 0.6
248
245
  need to get annotations for 6/6 joint igl clusters
249
- tag: v1.0.13
250
246
  annotate igh+igl: igl
251
247
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
252
248
  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/igh+igl/meta-igl.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml --ignore-sw-pair-info
@@ -276,4 +272,4 @@ hmm
276
272
  h 18 --> 21 +3
277
273
  k 6 --> 15 +9
278
274
  l 3 --> 6 +3
279
- total time: 16.3
275
+ total time: 15.4