partis-bcr 1.0.12.post1.dev1__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 (51) hide show
  1. packages/bpp/bin/bppseqgen +0 -0
  2. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/METADATA +1 -1
  3. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/RECORD +51 -50
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  5. test/new-results/partition-new-simu/fasttree/iclust-1/log +2 -2
  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 +48 -48
  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 +4 -4
  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+igl/partition-igh/fasttree/iclust-0/log +1 -1
  15. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +4 -4
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  31. test/paired/new-results/run-times.csv +6 -6
  32. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +64 -64
  33. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +71 -72
  34. test/paired/new-results/subset-partition-new-simu/merged-partition.log +39 -39
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  36. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  37. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  38. test/paired/new-results/test.log +148 -148
  39. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/gctree-run.py +0 -0
  44. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/parse-output.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/partis-test.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev1.data → partis_bcr-1.0.12.post1.dev3.data}/scripts/split-loci.py +0 -0
  48. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/WHEEL +0 -0
  49. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/entry_points.txt +0 -0
  50. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/licenses/COPYING +0 -0
  51. {partis_bcr-1.0.12.post1.dev1.dist-info → partis_bcr-1.0.12.post1.dev3.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -36,72 +36,72 @@ writing to paired subdirs
36
36
  run partis cache-parameters --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --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
37
37
  --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
38
38
  caching parameters
39
- vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.2 sec
39
+ vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.1 sec
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  keeping 6 / 198 v genes
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  smith-waterman (new-allele fitting)
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- vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
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+ vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
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43
  running 10 procs for 32 seqs
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  info for 32 / 32 = 1.000 (removed: 0 failed)
45
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  kept 14 (0.438) unproductive
46
- water time: 0.2 (ig-sw 0.1 processing 0.2)
46
+ water time: 0.1 (ig-sw 0.0 processing 0.1)
47
47
  smith-waterman (writing parameters)
48
- vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
48
+ vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
49
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  running 10 procs for 32 seqs
50
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  info for 32 / 32 = 1.000 (removed: 0 failed)
51
51
  kept 14 (0.438) unproductive
52
52
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
53
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (1.5 sec)
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- water time: 1.9 (ig-sw 1.7 processing 0.2)
53
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.8 sec)
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+ water time: 1.0 (ig-sw 0.9 processing 0.1)
55
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  writing hmms removed 18 genes from glfo (leaving v 6 d 16 j 4)
56
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
58
- (1.3 sec)
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+ (0.7 sec)
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  hmm
60
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  reading output
61
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  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (1.4 sec)
63
- infra time: 1.5
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- hmm step time: 3.7
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.7 sec)
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+ infra time: 0.8
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+ hmm step time: 1.4
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  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
66
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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- (0.9 sec)
69
- total time: 8.8
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+ (0.6 sec)
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+ total time: 4.4
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  cache-parameters igk:
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-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
72
72
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
73
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  caching parameters
74
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
74
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
75
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  keeping 5 / 64 v genes
76
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  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 0.0 sec
78
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  running 10 procs for 18 seqs
79
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  info for 18 / 18 = 1.000 (removed: 0 failed)
80
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  kept 9 (0.500) unproductive
81
- water time: 0.2 (ig-sw 0.0 processing 0.2)
81
+ water time: 0.1 (ig-sw 0.0 processing 0.1)
82
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  smith-waterman (writing parameters)
83
83
  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
84
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  running 10 procs for 18 seqs
85
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  info for 18 / 18 = 1.000 (removed: 0 failed)
86
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  kept 9 (0.500) unproductive
87
87
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
88
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (1.2 sec)
89
- water time: 1.5 (ig-sw 1.3 processing 0.1)
88
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.7 sec)
89
+ water time: 0.8 (ig-sw 0.7 processing 0.1)
90
90
  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
91
91
 
92
92
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
93
- (0.6 sec)
93
+ (0.4 sec)
94
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  hmm
95
95
  reading output
96
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  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
97
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (1.1 sec)
98
- infra time: 1.2
99
- hmm step time: 1.6
97
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.6 sec)
98
+ infra time: 0.7
99
+ hmm step time: 1.0
100
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  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
101
101
 
102
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
103
- (0.6 sec)
104
- total time: 5.0
103
+ (0.4 sec)
104
+ total time: 3.1
105
105
  cache-parameters igl:
106
106
  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
107
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  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -109,34 +109,34 @@ caching parameters
109
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  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
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  keeping 3 / 80 v genes
111
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  smith-waterman (new-allele fitting)
112
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
112
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
113
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  running 10 procs for 11 seqs
114
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  info for 11 / 11 = 1.000 (removed: 0 failed)
115
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  kept 7 (0.636) unproductive
116
- water time: 0.2 (ig-sw 0.0 processing 0.2)
116
+ water time: 0.1 (ig-sw 0.0 processing 0.1)
117
117
  smith-waterman (writing parameters)
118
118
  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
119
119
  running 10 procs for 11 seqs
120
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  info for 11 / 11 = 1.000 (removed: 0 failed)
121
121
  kept 7 (0.636) unproductive
122
122
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
123
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.8 sec)
124
- water time: 1.0 (ig-sw 0.9 processing 0.2)
123
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.4 sec)
124
+ water time: 0.6 (ig-sw 0.5 processing 0.2)
125
125
  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
126
126
 
127
127
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
128
- (0.5 sec)
128
+ (0.3 sec)
129
129
  hmm
130
130
  reading output
131
131
  read 11 hmm output lines with 11 sequences in 11 events (0 failures)
132
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.6 sec)
133
- infra time: 0.7
134
- hmm step time: 1.1
132
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.3 sec)
133
+ infra time: 0.4
134
+ hmm step time: 0.7
135
135
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
136
136
 
137
137
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
138
- (0.3 sec)
139
- total time: 3.7
138
+ (0.2 sec)
139
+ total time: 2.3
140
140
  partition igh:
141
141
  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-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/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
142
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  --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -148,66 +148,66 @@ smith-waterman
148
148
  kept 14 (0.438) unproductive
149
149
  water time: 0.0
150
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  hmm
151
- caching all 32 naive sequences (1.1s)
151
+ caching all 32 naive sequences (0.6s)
152
152
  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
153
- 30 clusters with 10 procs (0.5s)
154
- 29 clusters with 7 procs (0.6s)
155
- 28 clusters with 5 procs (0.5s)
156
- 28 clusters with 3 procs (0.7s)
157
- 23 clusters with 2 procs (0.8s)
158
- 20 clusters with 1 proc (1.1s)
153
+ 30 clusters with 10 procs (0.4s)
154
+ 29 clusters with 7 procs (0.5s)
155
+ 28 clusters with 5 procs (0.4s)
156
+ 28 clusters with 3 procs (0.4s)
157
+ 23 clusters with 2 procs (0.5s)
158
+ 20 clusters with 1 proc (0.8s)
159
159
  note not merging entire cpath history
160
- partition loop time: 4.2
160
+ partition loop time: 3.0
161
161
  getting annotations for final partition
162
- subcluster annotating 16 clusters with steps: (0.9s) (0.3s)
163
- subcluster annotation time 1.2
164
- total time: 6.7
162
+ subcluster annotating 16 clusters with steps: (0.5s) (0.2s)
163
+ subcluster annotation time 0.7
164
+ total time: 4.5
165
165
  partition igk:
166
166
  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
167
167
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
168
168
  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
169
169
  smith-waterman
170
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
170
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
171
171
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
172
172
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
173
173
  kept 9 (0.500) unproductive
174
174
  water time: 0.0
175
175
  hmm
176
- caching all 18 naive sequences (0.5s)
176
+ caching all 18 naive sequences (0.4s)
177
177
  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
178
178
  reducing n procs to number of clusters: 10 --> 7
179
179
  7 clusters with 7 procs (0.3s)
180
- 7 clusters with 5 procs (0.3s)
181
- 7 clusters with 3 procs (0.3s)
180
+ 7 clusters with 5 procs (0.2s)
181
+ 7 clusters with 3 procs (0.2s)
182
182
  6 clusters with 2 procs (0.2s)
183
- 6 clusters with 1 proc (0.5s)
184
- partition loop time: 1.6
183
+ 6 clusters with 1 proc (0.3s)
184
+ partition loop time: 1.2
185
185
  getting annotations for final partition
186
- subcluster annotating 6 clusters with steps: (0.4s) (0.1s)
187
- subcluster annotation time 0.5
188
- total time: 2.7
186
+ subcluster annotating 6 clusters with steps: (0.3s) (0.1s)
187
+ subcluster annotation time 0.4
188
+ total time: 2.2
189
189
  partition igl:
190
190
  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
191
191
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
192
192
  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
193
193
  smith-waterman
194
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
194
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
195
195
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
196
196
  info for 11 / 11 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
197
197
  kept 7 (0.636) unproductive
198
198
  water time: 0.0
199
199
  hmm
200
- caching all 11 naive sequences (0.5s)
200
+ caching all 11 naive sequences (0.2s)
201
201
  collapsed 11 queries into 3 clusters with identical naive seqs (0.0 sec)
202
202
  reducing n procs to number of clusters: 10 --> 3
203
- 3 clusters with 3 procs (0.3s)
203
+ 3 clusters with 3 procs (0.2s)
204
204
  3 clusters with 2 procs (0.2s)
205
205
  3 clusters with 1 proc (0.3s)
206
- partition loop time: 0.7
206
+ partition loop time: 0.6
207
207
  getting annotations for final partition
208
- subcluster annotating 3 clusters with steps: (0.3s) (0.2s)
209
- subcluster annotation time 0.4
210
- total time: 1.8
208
+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
209
+ subcluster annotation time 0.3
210
+ total time: 1.4
211
211
  combining chains
212
212
  cleaning pair info for 61 seqs
213
213
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -233,15 +233,15 @@ cleaning pair info for 61 seqs
233
233
  --input-partition-fname: read best partition with 19 sequences in 11 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
234
234
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
235
235
  smith-waterman
236
- vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.2 sec
236
+ vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.1 sec
237
237
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
238
238
  info for 19 / 19 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
239
239
  kept 7 (0.368) unproductive
240
240
  water time: 0.0
241
241
  hmm
242
- subcluster annotating 11 clusters with steps: (0.7s) (0.2s)
243
- subcluster annotation time 0.9
244
- total time: 1.1
242
+ subcluster annotating 11 clusters with steps: (0.4s) (0.2s)
243
+ subcluster annotation time 0.6
244
+ total time: 0.7
245
245
  need to get annotations for 6/11 joint igk clusters
246
246
  annotate igh+igk: igk
247
247
  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
@@ -257,9 +257,8 @@ smith-waterman
257
257
  hmm
258
258
  reading output
259
259
  read 11 hmm output lines with 18 sequences in 11 events (0 failures)
260
- infra time: 0.1
261
- hmm step time: 0.5
262
- total time: 0.6
260
+ hmm step time: 0.3
261
+ total time: 0.5
263
262
  igh+igl: synchronizing heavy and light chain cluster paths
264
263
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
265
264
  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
@@ -288,9 +287,9 @@ smith-waterman
288
287
  kept 7 (0.583) unproductive
289
288
  water time: 0.0
290
289
  hmm
291
- subcluster annotating 5 clusters with steps: (0.4s) (0.4s)
292
- subcluster annotation time 0.8
293
- total time: 1.0
290
+ subcluster annotating 5 clusters with steps: (0.3s) (0.3s)
291
+ subcluster annotation time 0.6
292
+ total time: 0.7
294
293
  need to get annotations for 5/5 joint igl clusters
295
294
  annotate igh+igl: igl
296
295
  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
@@ -304,7 +303,7 @@ smith-waterman
304
303
  kept 7 (0.636) unproductive
305
304
  water time: 0.0
306
305
  hmm
307
- subcluster annotating 5 clusters with steps: (0.4s) (0.2s)
306
+ subcluster annotating 5 clusters with steps: (0.2s) (0.3s)
308
307
  subcluster annotation time 0.5
309
308
  total time: 0.6
310
309
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
@@ -319,4 +318,4 @@ hmm
319
318
  h 16 --> 16
320
319
  k 6 --> 11 +5
321
320
  l 3 --> 5 +2
322
- total time: 66.7
321
+ total time: 39.9
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -17,7 +17,7 @@ partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/
17
17
  removed 3/56 queries from input info that were absent from input partition
18
18
  partitioning (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
19
19
  smith-waterman
20
- vsearch: 53 / 53 v annotations (0 failed) with 6 v genes in 0.2 sec
20
+ vsearch: 53 / 53 v annotations (0 failed) with 6 v genes in 0.1 sec
21
21
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
22
22
  info for 53 / 53 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
23
23
  kept 24 (0.453) unproductive
@@ -27,16 +27,16 @@ hmm
27
27
  caching input annotation naive seqs in bcrham cache file for 27 clusters (53 seqs)
28
28
  --continue-from-input-partition: using input partition for initial cpath
29
29
  27 clusters (53 seqs)
30
- 27 clusters with 10 procs (0.9s)
31
- 26 clusters with 7 procs (0.7s)
32
- 23 clusters with 5 procs (0.6s)
33
- 22 clusters with 3 procs (0.6s)
34
- 21 clusters with 2 procs (0.4s)
35
- 21 clusters with 1 proc (0.9s)
36
- partition loop time: 4.1
30
+ 27 clusters with 10 procs (0.5s)
31
+ 26 clusters with 7 procs (0.5s)
32
+ 23 clusters with 5 procs (0.4s)
33
+ 22 clusters with 3 procs (0.4s)
34
+ 21 clusters with 2 procs (0.3s)
35
+ 21 clusters with 1 proc (0.7s)
36
+ partition loop time: 2.8
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (1.0s) (0.4s) (0.3s)
39
- subcluster annotation time 1.7
38
+ subcluster annotating 18 clusters with steps: (0.7s) (0.4s) (0.2s)
39
+ subcluster annotation time 1.3
40
40
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
41
41
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
42
42
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
@@ -47,7 +47,7 @@ getting annotations for final partition
47
47
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
48
48
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
49
49
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
50
- total time: 6.3
50
+ total time: 4.3
51
51
  partition igk:
52
52
  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igk.yaml --continue-from-input-partition --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/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
53
53
  warning replacing 'paired-uids'/'paired-uids' value for 'bc11af4843-igk' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['bc11af4843-igh', 'eee6809ad6-igh', 'eee6809ad6-igl'] --> ['eee6809ad6-igh']
@@ -63,7 +63,7 @@ getting annotations for final partition
63
63
  --input-partition-fname: read best partition with 36 sequences in 19 clusters from test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igk.yaml
64
64
  partitioning (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm)
65
65
  smith-waterman
66
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
66
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
67
67
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
68
68
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
69
69
  kept 14 (0.389) unproductive
@@ -75,16 +75,16 @@ hmm
75
75
  19 clusters (36 seqs)
76
76
  19 clusters with 10 procs (0.3s)
77
77
  17 clusters with 7 procs (0.3s)
78
- 15 clusters with 5 procs (0.2s)
79
- 12 clusters with 3 procs (0.2s)
78
+ 15 clusters with 5 procs (0.3s)
79
+ 12 clusters with 3 procs (0.3s)
80
80
  11 clusters with 2 procs (0.2s)
81
81
  7 clusters with 1 proc (0.4s)
82
82
  note not merging entire cpath history
83
- partition loop time: 1.6
83
+ partition loop time: 1.8
84
84
  getting annotations for final partition
85
- subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.1s)
86
- subcluster annotation time 0.9
87
- total time: 2.9
85
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.2s)
86
+ subcluster annotation time 0.8
87
+ total time: 2.8
88
88
  partition igl:
89
89
  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igl.yaml --continue-from-input-partition --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/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
90
90
  warning replacing 'paired-uids'/'paired-uids' value for '7588f09c07-igl' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['7588f09c07-igh', 'cb8a759f1a-igh'] --> ['7588f09c07-igh']
@@ -113,23 +113,23 @@ hmm
113
113
  --continue-from-input-partition: using input partition for initial cpath
114
114
  8 clusters (18 seqs)
115
115
  reducing n procs to number of clusters: 10 --> 8
116
- 8 clusters with 8 procs (0.3s)
116
+ 8 clusters with 8 procs (0.2s)
117
117
  8 clusters with 6 procs (0.3s)
118
- 7 clusters with 4 procs (0.3s)
118
+ 7 clusters with 4 procs (0.2s)
119
119
  6 clusters with 3 procs (0.2s)
120
120
  6 clusters with 2 procs (0.2s)
121
- 3 clusters with 1 proc (0.3s)
122
- partition loop time: 1.6
121
+ 3 clusters with 1 proc (0.2s)
122
+ partition loop time: 1.3
123
123
  getting annotations for final partition
124
- subcluster annotating 3 clusters with steps: (0.3s) (0.2s) (0.1s)
125
- subcluster annotation time 0.7
124
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s) (0.2s)
125
+ subcluster annotation time 0.6
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
129
129
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
130
130
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
131
131
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
132
- total time: 2.5
132
+ total time: 2.0
133
133
  combining chains
134
134
  cleaning pair info for 107 seqs
135
135
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -172,15 +172,15 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
172
172
  --input-partition-fname: read best partition with 35 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml
173
173
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
174
174
  smith-waterman
175
- vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.2 sec
175
+ vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.1 sec
176
176
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
177
177
  info for 35 / 35 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
178
178
  kept 13 (0.371) unproductive
179
179
  water time: 0.0
180
180
  hmm
181
- subcluster annotating 15 clusters with steps: (0.7s) (0.3s)
182
- subcluster annotation time 1.0
183
- total time: 1.3
181
+ subcluster annotating 15 clusters with steps: (0.5s) (0.3s)
182
+ subcluster annotation time 0.8
183
+ total time: 1.0
184
184
  need to get annotations for 13/15 joint igk clusters
185
185
  annotate igh+igk: igk
186
186
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
@@ -189,15 +189,15 @@ hmm
189
189
  --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml
190
190
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm)
191
191
  smith-waterman
192
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
192
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
193
193
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
194
194
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
195
195
  kept 14 (0.389) unproductive
196
196
  water time: 0.0
197
197
  hmm
198
- subcluster annotating 15 clusters with steps: (0.7s) (0.2s)
199
- subcluster annotation time 0.9
200
- total time: 1.2
198
+ subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
199
+ subcluster annotation time 0.7
200
+ total time: 0.9
201
201
  igh+igl: synchronizing heavy and light chain cluster paths
202
202
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
203
203
  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
@@ -239,8 +239,8 @@ smith-waterman
239
239
  kept 11 (0.579) unproductive
240
240
  water time: 0.0
241
241
  hmm
242
- subcluster annotating 6 clusters with steps: (0.4s) (0.3s) (0.4s)
243
- subcluster annotation time 1.1
242
+ subcluster annotating 6 clusters with steps: (0.4s) (0.3s) (0.3s)
243
+ subcluster annotation time 1.0
244
244
  total time: 1.2
245
245
  need to get annotations for 6/6 joint igl clusters
246
246
  annotate igh+igl: igl
@@ -256,9 +256,9 @@ smith-waterman
256
256
  kept 13 (0.722) unproductive
257
257
  water time: 0.0
258
258
  hmm
259
- subcluster annotating 6 clusters with steps: (0.3s) (0.2s) (0.2s)
260
- subcluster annotation time 0.7
261
- total time: 0.8
259
+ subcluster annotating 6 clusters with steps: (0.3s) (0.2s) (0.1s)
260
+ subcluster annotation time 0.6
261
+ total time: 0.7
262
262
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml
263
263
  concatenating heavy chain loci:
264
264
  h starting with 15 annotations (35 seqs)
@@ -272,4 +272,4 @@ hmm
272
272
  h 18 --> 21 +3
273
273
  k 6 --> 15 +9
274
274
  l 3 --> 6 +3
275
- total time: 36.4
275
+ total time: 26.5