partis-bcr 1.0.12.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13__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 (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
test/paired/new-results/test.log CHANGED
@@ -5,7 +5,7 @@
5
5
  run partis cache-parameters --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
6
6
  --input-metafnames: added meta info for 56 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
7
7
  caching parameters
8
- vsearch: 56 / 56 v annotations (0 failed) with 9 v genes in 0.1 sec
8
+ vsearch: 56 / 56 v annotations (0 failed) with 9 v genes in 0.2 sec
9
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  keeping 6 / 198 v genes
10
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  missing 17 simulation genes (counts): hv1-1801 0 hv1-4603 0 hv1-801 0 hv2-502 0 hv3-1101 0 hv3-1501 0 hv3-2001 0 hv3-2101 0 hv3-2301 0 hv3-3004 0 hv3-4802 0 hv3-6601 0 hv3-7401 0 hv3-901 0 hv4-3103 0 hv4-402 0 hv4-5911 0
11
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  smith-waterman (new-allele fitting)
@@ -13,46 +13,46 @@ smith-waterman (new-allele fitting)
13
13
  running 10 procs for 56 seqs
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  info for 56 / 56 = 1.000 (removed: 0 failed)
15
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  kept 25 (0.446) unproductive
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- water time: 0.2 (ig-sw 0.1 processing 0.2)
16
+ water time: 0.3 (ig-sw 0.1 processing 0.2)
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  smith-waterman (writing parameters)
18
- vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.2 sec
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+ vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.4 sec
19
19
  running 10 procs for 56 seqs
20
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  info for 56 / 56 = 1.000 (removed: 0 failed)
21
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  kept 25 (0.446) unproductive
22
22
  writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
23
- writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (1.4 sec)
24
- water time: 1.9 (ig-sw 1.7 processing 0.2)
23
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (2.1 sec)
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+ water time: 2.5 (ig-sw 2.3 processing 0.2)
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  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
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27
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
28
- (1.0 sec)
28
+ (1.2 sec)
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  hmm
30
30
  reading output
31
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  read 56 hmm output lines with 56 sequences in 56 events (0 failures)
32
- writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (1.2 sec)
33
- writing parameters to test/paired/new-results/test/parameters/simu/igh/true (1.1 sec)
34
- infra time: 2.5
35
- hmm step time: 4.1
32
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (1.5 sec)
33
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/true (2.0 sec)
34
+ infra time: 3.8
35
+ hmm step time: 5.3
36
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  writing hmms removed 3 genes from glfo (leaving v 6 d 15 j 4)
37
37
 
38
38
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
39
- (1.0 sec)
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- total time: 9.0
39
+ (2.2 sec)
40
+ total time: 12.7
41
41
  cache-parameters igk:
42
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  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
43
43
  run partis cache-parameters --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
44
44
  --input-metafnames: added meta info for 36 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
45
45
  caching parameters
46
- vsearch: 36 / 36 v annotations (0 failed) with 6 v genes in 0.1 sec
46
+ vsearch: 36 / 36 v annotations (0 failed) with 6 v genes in 0.2 sec
47
47
  keeping 5 / 64 v genes
48
48
  missing 11 simulation genes (counts): kv1-1201 0 kv1-2701 0 kv1-501 0 kv1-803 0 kv1-901 0 kv1D-3901 0 kv2-2401 0 kv2D-2801 0 kv3-2001 0 kv4-102 0 kv6-2101 0
49
49
  smith-waterman (new-allele fitting)
50
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
50
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
51
51
  running 10 procs for 36 seqs
52
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  running 11 procs for 2 seqs
53
53
  info for 36 / 36 = 1.000 (removed: 0 failed)
54
54
  kept 14 (0.389) unproductive
55
- water time: 0.4 (ig-sw 0.0 processing 0.1)
55
+ water time: 0.4 (ig-sw 0.0 processing 0.2)
56
56
  smith-waterman (writing parameters)
57
57
  vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
58
58
  running 10 procs for 36 seqs
@@ -60,24 +60,24 @@ smith-waterman (writing parameters)
60
60
  info for 36 / 36 = 1.000 (removed: 0 failed)
61
61
  kept 14 (0.389) unproductive
62
62
  writing sw results to test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
63
- writing parameters to test/paired/new-results/test/parameters/simu/igk/sw (1.1 sec)
64
- water time: 1.6 (ig-sw 1.2 processing 0.1)
63
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/sw (1.2 sec)
64
+ water time: 1.7 (ig-sw 1.3 processing 0.2)
65
65
  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
66
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67
67
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
68
- (1.2 sec)
68
+ (0.8 sec)
69
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  hmm
70
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  reading output
71
71
  read 36 hmm output lines with 36 sequences in 36 events (0 failures)
72
- writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.9 sec)
72
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (1.1 sec)
73
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  writing parameters to test/paired/new-results/test/parameters/simu/igk/true (1.3 sec)
74
- infra time: 2.5
75
- hmm step time: 3.7
74
+ infra time: 2.7
75
+ hmm step time: 3.9
76
76
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
77
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78
78
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
79
- (1.8 sec)
80
- total time: 9.3
79
+ (0.7 sec)
80
+ total time: 8.2
81
81
  cache-parameters igl:
82
82
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
83
83
  run partis cache-parameters --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -87,7 +87,7 @@ caching parameters
87
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  keeping 3 / 80 v genes
88
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  missing 7 simulation genes (counts): lv1-5102 0 lv3-101 0 lv3-1901 0 lv3-2701 0 lv4-6003 0 lv7-4604 0 lv8-6101 0
89
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  smith-waterman (new-allele fitting)
90
- vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.1 sec
90
+ vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.2 sec
91
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  running 10 procs for 21 seqs
92
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  info for 21 / 21 = 1.000 (removed: 0 failed)
93
93
  kept 14 (0.667) unproductive
@@ -98,8 +98,8 @@ smith-waterman (writing parameters)
98
98
  info for 21 / 21 = 1.000 (removed: 0 failed)
99
99
  kept 14 (0.667) unproductive
100
100
  writing sw results to test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
101
- writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.5 sec)
102
- water time: 0.8 (ig-sw 0.6 processing 0.2)
101
+ writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.7 sec)
102
+ water time: 1.0 (ig-sw 0.8 processing 0.2)
103
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  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
104
104
 
105
105
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -107,16 +107,16 @@ smith-waterman (writing parameters)
107
107
  hmm
108
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  reading output
109
109
  read 21 hmm output lines with 21 sequences in 21 events (0 failures)
110
- writing parameters to test/paired/new-results/test/parameters/simu/igl/hmm (0.4 sec)
111
- writing parameters to test/paired/new-results/test/parameters/simu/igl/true (0.5 sec)
112
- infra time: 1.1
113
- hmm step time: 1.6
110
+ writing parameters to test/paired/new-results/test/parameters/simu/igl/hmm (0.6 sec)
111
+ writing parameters to test/paired/new-results/test/parameters/simu/igl/true (0.8 sec)
112
+ infra time: 1.6
113
+ hmm step time: 2.0
114
114
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
115
115
 
116
116
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
117
- (0.3 sec)
118
- total time: 3.8
119
- total time: 31.8
117
+ (0.4 sec)
118
+ total time: 4.5
119
+ total time: 36.1
120
120
  partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu
121
121
  warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
122
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  partition igh:
@@ -125,7 +125,7 @@ hmm
125
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  --input-metafnames: added meta info for 56 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
126
126
  partitioning (with test/paired/new-results/test/parameters/simu/igh/hmm)
127
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  smith-waterman
128
- vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.1 sec
128
+ vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.2 sec
129
129
  reading sw results from test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
130
130
  info for 56 / 56 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
131
131
  kept 25 (0.446) unproductive
@@ -134,50 +134,50 @@ smith-waterman
134
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  (0.0 sec)
135
135
  water time: 0.3
136
136
  hmm
137
- caching all 56 naive sequences (1.6s)
137
+ caching all 56 naive sequences (1.7s)
138
138
  collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
139
- 50 clusters with 10 procs (1.0s)
140
- 44 clusters with 7 procs (0.9s)
141
- 36 clusters with 5 procs (0.8s)
142
- 31 clusters with 3 procs (0.6s)
143
- 29 clusters with 2 procs (0.9s)
144
- 23 clusters with 1 proc (1.0s)
139
+ 50 clusters with 10 procs (0.9s)
140
+ 44 clusters with 7 procs (0.7s)
141
+ 36 clusters with 5 procs (0.7s)
142
+ 31 clusters with 3 procs (0.5s)
143
+ 29 clusters with 2 procs (1.1s)
144
+ 23 clusters with 1 proc (1.5s)
145
145
  note not merging entire cpath history
146
- partition loop time: 5.3
146
+ partition loop time: 5.4
147
147
  getting annotations for final partition
148
- subcluster annotating 20 clusters with steps: (1.0s) (0.4s) plotting performance
148
+ subcluster annotating 20 clusters with steps: (1.0s) (0.5s) plotting performance
149
149
  warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
150
150
  (0.0 sec)
151
151
 
152
152
  subcluster annotation time 1.6
153
- total time: 8.9
153
+ total time: 9.5
154
154
  partition igk:
155
155
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
156
156
  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igk --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
157
157
  --input-metafnames: added meta info for 36 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
158
158
  partitioning (with test/paired/new-results/test/parameters/simu/igk/hmm)
159
159
  smith-waterman
160
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
160
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
161
161
  reading sw results from test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
162
162
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
163
163
  kept 14 (0.389) unproductive
164
164
  plotting performance (0.0 sec)
165
165
  water time: 0.2
166
166
  hmm
167
- caching all 36 naive sequences (0.8s)
167
+ caching all 36 naive sequences (0.7s)
168
168
  collapsed 36 queries into 7 clusters with identical naive seqs (0.0 sec)
169
169
  reducing n procs to number of clusters: 10 --> 7
170
170
  7 clusters with 7 procs (0.3s)
171
- 7 clusters with 5 procs (0.4s)
171
+ 7 clusters with 5 procs (0.3s)
172
172
  7 clusters with 3 procs (0.3s)
173
173
  7 clusters with 2 procs (0.3s)
174
- 6 clusters with 1 proc (0.4s)
175
- partition loop time: 1.7
174
+ 6 clusters with 1 proc (0.5s)
175
+ partition loop time: 1.6
176
176
  getting annotations for final partition
177
- subcluster annotating 6 clusters with steps: (0.5s) (0.2s) (0.2s) plotting performance (0.0 sec)
177
+ subcluster annotating 6 clusters with steps: (0.8s) (0.2s) (0.2s) plotting performance (0.0 sec)
178
178
 
179
- subcluster annotation time 1.0
180
- total time: 3.7
179
+ subcluster annotation time 1.3
180
+ total time: 4.0
181
181
  partition igl:
182
182
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
183
183
  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igl --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -194,15 +194,15 @@ hmm
194
194
  caching all 21 naive sequences (0.5s)
195
195
  collapsed 21 queries into 3 clusters with identical naive seqs (0.0 sec)
196
196
  reducing n procs to number of clusters: 10 --> 3
197
- 3 clusters with 3 procs (0.2s)
197
+ 3 clusters with 3 procs (0.3s)
198
198
  3 clusters with 2 procs (0.2s)
199
199
  3 clusters with 1 proc (0.3s)
200
200
  partition loop time: 0.7
201
201
  getting annotations for final partition
202
- subcluster annotating 3 clusters with steps: (0.4s) (0.2s) (0.2s) plotting performance (0.0 sec)
202
+ subcluster annotating 3 clusters with steps: (0.3s) (0.2s) (0.3s) plotting performance (0.0 sec)
203
203
 
204
- subcluster annotation time 0.8
205
- total time: 2.2
204
+ subcluster annotation time 0.9
205
+ total time: 2.4
206
206
  combining chains
207
207
  cleaning pair info for 113 seqs
208
208
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -240,6 +240,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
240
240
  joint 0.963 0.594
241
241
  merge time 0.0
242
242
  need to get annotations for 7/15 joint igh clusters
243
+ tag: v1.0.13
243
244
  annotate igh+igk: igh
244
245
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
245
246
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
@@ -253,10 +254,11 @@ smith-waterman
253
254
  kept 13 (0.361) unproductive
254
255
  water time: 0.0
255
256
  hmm
256
- subcluster annotating 15 clusters with steps: (0.8s) (0.3s)
257
- subcluster annotation time 1.1
258
- total time: 1.3
257
+ subcluster annotating 15 clusters with steps: (0.6s) (0.3s)
258
+ subcluster annotation time 0.9
259
+ total time: 1.1
259
260
  need to get annotations for 13/15 joint igk clusters
261
+ tag: v1.0.13
260
262
  annotate igh+igk: igk
261
263
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
262
264
  run partis annotate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igk.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
@@ -298,6 +300,7 @@ hmm
298
300
  joint 1.000 0.611
299
301
  merge time 0.0
300
302
  need to get annotations for 5/8 joint igh clusters
303
+ tag: v1.0.13
301
304
  annotate igh+igl: igh
302
305
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
303
306
  run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
@@ -311,10 +314,11 @@ smith-waterman
311
314
  kept 12 (0.600) unproductive
312
315
  water time: 0.0
313
316
  hmm
314
- subcluster annotating 8 clusters with steps: (0.7s) (0.3s)
317
+ subcluster annotating 8 clusters with steps: (0.6s) (0.3s)
315
318
  subcluster annotation time 0.9
316
- total time: 1.0
319
+ total time: 1.1
317
320
  need to get annotations for 8/8 joint igl clusters
321
+ tag: v1.0.13
318
322
  annotate igh+igl: igl
319
323
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
320
324
  run partis annotate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igl.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
@@ -322,13 +326,13 @@ hmm
322
326
  --input-partition-fname: read best partition with 21 sequences in 8 clusters from test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
323
327
  annotating (with test/paired/new-results/test/parameters/simu/igl/hmm)
324
328
  smith-waterman
325
- vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.1 sec
329
+ vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.2 sec
326
330
  reading sw results from test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
327
331
  info for 21 / 21 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
328
332
  kept 14 (0.667) unproductive
329
333
  water time: 0.0
330
334
  hmm
331
- subcluster annotating 8 clusters with steps: (0.5s) (0.2s)
335
+ subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
332
336
  subcluster annotation time 0.7
333
337
  total time: 0.9
334
338
  concatenating heavy chain loci:
@@ -343,7 +347,7 @@ hmm
343
347
  h 20 --> 23 +3
344
348
  k 6 --> 15 +9
345
349
  l 3 --> 8 +5
346
- total time: 39.6
350
+ total time: 43.8
347
351
  subset-partition-new-simu partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
348
352
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
349
353
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -372,9 +376,12 @@ hmm
372
376
  writing merged outputs from 2 subsets to test/paired/new-results/subset-partition-new-simu/merged-subsets
373
377
  writing combined h/l info to fasta and meta files in test/paired/new-results/subset-partition-new-simu/merged-subsets
374
378
  merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
379
+ tag: v1.0.13
380
+ tag: v1.0.13
381
+ tag: v1.0.13
375
382
  run partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --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 --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
376
383
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
377
- total time: 152.8
384
+ total time: 177.4
378
385
  seed-partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
379
386
  removing seqs very different from seed seq
380
387
  wrong/no removed singly kept missing
@@ -399,27 +406,27 @@ smith-waterman
399
406
  kept 8 (0.471) unproductive
400
407
  water time: 0.0
401
408
  hmm
402
- caching all 17 naive sequences (0.6s)
409
+ caching all 17 naive sequences (0.7s)
403
410
  collapsed 17 queries into 17 clusters with identical naive seqs (0.0 sec)
404
411
  17 clusters with 10 procs (0.5s)
405
- 17 clusters with 7 procs (0.4s)
406
- 17 clusters with 5 procs (0.4s)
407
- 17 clusters with 3 procs (0.4s)
408
- 14 clusters with 2 procs (0.4s)
412
+ 17 clusters with 7 procs (0.5s)
413
+ 17 clusters with 5 procs (0.5s)
414
+ 17 clusters with 3 procs (0.6s)
415
+ 14 clusters with 2 procs (0.5s)
409
416
  14 clusters with 1 proc (0.7s)
410
- partition loop time: 2.9
417
+ partition loop time: 3.2
411
418
  getting annotations for final partition
412
419
  reading output
413
420
  read 12 hmm output lines with 17 sequences in 12 events (0 failures)
414
- hmm step time: 0.6
415
- total time: 4.4
421
+ hmm step time: 0.5
422
+ total time: 4.6
416
423
  partition igk:
417
424
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
418
425
  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
419
426
  --input-metafnames: added meta info for 12 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
420
427
  partitioning (with test/paired/new-results/test/parameters/simu/igk/hmm)
421
428
  smith-waterman
422
- vsearch: 12 / 12 v annotations (0 failed) with 2 v genes in 0.1 sec
429
+ vsearch: 12 / 12 v annotations (0 failed) with 2 v genes in 0.2 sec
423
430
  reading sw results from test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
424
431
  info for 12 / 12 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
425
432
  kept 7 (0.583) unproductive
@@ -428,14 +435,14 @@ hmm
428
435
  caching all 12 naive sequences (0.4s)
429
436
  collapsed 12 queries into 3 clusters with identical naive seqs (0.0 sec)
430
437
  reducing n procs to number of clusters: 10 --> 3
431
- 3 clusters with 3 procs (0.3s)
432
- 3 clusters with 2 procs (0.2s)
438
+ 3 clusters with 3 procs (0.2s)
439
+ 3 clusters with 2 procs (0.1s)
433
440
  3 clusters with 1 proc (0.2s)
434
- partition loop time: 0.7
441
+ partition loop time: 0.6
435
442
  getting annotations for final partition
436
- subcluster annotating 2 clusters with steps: (0.3s) (0.1s) (0.2s)
437
- subcluster annotation time 0.6
438
- total time: 1.8
443
+ subcluster annotating 2 clusters with steps: (0.3s) (0.2s) (0.2s)
444
+ subcluster annotation time 0.7
445
+ total time: 1.9
439
446
  partition igl:
440
447
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
441
448
  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igl.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -448,12 +455,12 @@ smith-waterman
448
455
  info for 4 / 4 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
449
456
  water time: 0.0
450
457
  hmm
451
- caching all 4 naive sequences (0.2s)
458
+ caching all 4 naive sequences (0.3s)
452
459
  collapsed 4 queries into 2 clusters with identical naive seqs (0.0 sec)
453
460
  reducing n procs to number of clusters: 4 --> 2
454
461
  2 clusters with 2 procs (0.2s)
455
462
  2 clusters with 1 proc (0.3s)
456
- partition loop time: 0.5
463
+ partition loop time: 0.4
457
464
  getting annotations for final partition
458
465
  reading output
459
466
  read 2 hmm output lines with 4 sequences in 2 events (0 failures)
@@ -497,6 +504,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
497
504
  merge time 0.0
498
505
  removed 7 unseeded clusters (of 8 total, leaving 1) from igh joint partition
499
506
  seed cluster size in best joint partition: 1, excluding seed seq: 0
507
+ tag: v1.0.13
500
508
  annotate igh+igk: igh
501
509
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
502
510
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -513,11 +521,12 @@ smith-waterman
513
521
  hmm
514
522
  reading output
515
523
  read 1 hmm output lines with 1 sequences in 1 events (0 failures)
516
- hmm step time: 0.2
524
+ hmm step time: 0.3
517
525
  total time: 0.4
518
526
  removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
519
527
  need to get annotations for 1/1 joint igk clusters
520
528
  seed cluster size in best joint partition: 1, excluding seed seq: 0
529
+ tag: v1.0.13
521
530
  annotate igh+igk: igk
522
531
  removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
523
532
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -535,7 +544,7 @@ smith-waterman
535
544
  hmm
536
545
  reading output
537
546
  read 1 hmm output lines with 1 sequences in 1 events (0 failures)
538
- hmm step time: 0.1
547
+ hmm step time: 0.2
539
548
  total time: 0.3
540
549
  igh+igl: synchronizing heavy and light chain cluster paths
541
550
  removing badly + unpaired seqs: kept 1 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 1 l 0
@@ -564,7 +573,7 @@ hmm
564
573
  N clusters with all seqs:
565
574
  h 12 --> 1 -11
566
575
  k 2 --> 1 -1
567
- total time: 20.3
576
+ total time: 23.9
568
577
  get-selection-metrics-new-simu partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
569
578
  get-selection-metrics igh+igk: igh
570
579
  run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -577,7 +586,7 @@ hmm
577
586
  starting 2 jobs
578
587
  run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa
579
588
  run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa
580
- made 2 fasttree trees (0.2s)
589
+ made 2 fasttree trees (0.3s)
581
590
  tree origins: 2 ran fasttree
582
591
  skipped 3/5 clusters smaller than 4
583
592
  setting default tau to 1 / 385 = 0.0026
@@ -685,10 +694,10 @@ hmm
685
694
  skipped 1/4 clusters that had no uids in common with tree
686
695
  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
687
696
  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
688
- total time: 14.0
697
+ total time: 12.6
689
698
  cache-parameters-data partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
690
699
  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
691
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/114321/meta.yaml --n-max-queries 100
700
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/263977/meta.yaml --n-max-queries 100
692
701
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
693
702
  extract_pairing_info(): read 100 sequences with 48 droplet ids
694
703
  droplet id separators (set automatically): _ indices: [0]
@@ -699,14 +708,14 @@ hmm
699
708
  2 42 0.875
700
709
  3 2 0.042
701
710
  4 2 0.042
702
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/114321 --input-metafname /tmp/runner/hmms/114321/meta.yaml --n-max-queries 100
711
+ run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/263977 --input-metafname /tmp/runner/hmms/263977/meta.yaml --n-max-queries 100
703
712
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
704
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/114321/meta.yaml: paired-uids
713
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/263977/meta.yaml: paired-uids
705
714
  read pairing info for 100 seqs from input meta file
706
715
  running vsearch on 100 sequences:
707
- igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
708
- igk: 40 / 100 v annotations (60 failed) with 18 v genes in 0.1 sec
709
- igl: 15 / 100 v annotations (85 failed) with 12 v genes in 0.1 sec
716
+ igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.3 sec
717
+ igk: 40 / 100 v annotations (60 failed) with 18 v genes in 0.2 sec
718
+ igl: 15 / 100 v annotations (85 failed) with 12 v genes in 0.2 sec
710
719
  totals: igh 48 igk 37 igl 15
711
720
  count frac paired with
712
721
  h 31 0.65 k
@@ -724,10 +733,10 @@ totals: igh 48 igk 37 igl 15
724
733
  2 0.13 h l
725
734
  1 0.07 h k
726
735
  1 0.07 h h k
727
- writing to /tmp/runner/hmms/114321/
728
- igh: 48 to 114321/igh.fa
729
- igk: 37 to 114321/igk.fa
730
- igl: 15 to 114321/igl.fa
736
+ writing to /tmp/runner/hmms/263977/
737
+ igh: 48 to 263977/igh.fa
738
+ igk: 37 to 263977/igk.fa
739
+ igl: 15 to 263977/igl.fa
731
740
  writing to paired subdirs
732
741
  igh+igk:
733
742
  igh: 36 / 48 to igh+igk/igh.fa
@@ -736,25 +745,25 @@ writing to paired subdirs
736
745
  igh: 15 / 48 to igh+igl/igh.fa
737
746
  igl: 15 / 15 to igh+igl/igl.fa
738
747
  cache-parameters igh:
739
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/114321/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/114321/meta.yaml
740
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/114321/meta.yaml: paired-uids
748
+ run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/263977/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/263977/meta.yaml
749
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/263977/meta.yaml: paired-uids
741
750
  caching parameters
742
751
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.1 sec
743
752
  keeping 23 / 198 v genes
744
753
  smith-waterman (new-allele fitting)
745
- vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.1 sec
754
+ vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.2 sec
746
755
  running 10 procs for 48 seqs
747
756
  info for 48 / 48 = 1.000 (removed: 0 failed)
748
757
  kept 1 (0.021) unproductive
749
- water time: 0.3 (ig-sw 0.0 processing 0.3)
758
+ water time: 0.3 (ig-sw 0.1 processing 0.3)
750
759
  smith-waterman (writing parameters)
751
- vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.1 sec
760
+ vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.2 sec
752
761
  running 10 procs for 48 seqs
753
762
  info for 48 / 48 = 1.000 (removed: 0 failed)
754
763
  kept 1 (0.021) unproductive
755
764
  writing sw results to test/paired/new-results/test/parameters/data/igh/sw-cache.yaml
756
- writing parameters to test/paired/new-results/test/parameters/data/igh/sw (3.6 sec)
757
- water time: 4.0 (ig-sw 3.8 processing 0.2)
765
+ writing parameters to test/paired/new-results/test/parameters/data/igh/sw (6.4 sec)
766
+ water time: 6.9 (ig-sw 6.6 processing 0.3)
758
767
  writing hmms removed 13 genes from glfo (leaving v 23 d 19 j 6)
759
768
 
760
769
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -762,17 +771,17 @@ smith-waterman (writing parameters)
762
771
  hmm
763
772
  reading output
764
773
  read 48 hmm output lines with 48 sequences in 48 events (0 failures)
765
- writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (3.6 sec)
766
- infra time: 3.8
767
- hmm step time: 5.3
774
+ writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (4.8 sec)
775
+ infra time: 5.0
776
+ hmm step time: 6.3
768
777
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
769
778
 
770
779
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
771
- (2.7 sec)
772
- total time: 15.8
780
+ (2.4 sec)
781
+ total time: 19.9
773
782
  cache-parameters igk:
774
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/114321/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/114321/meta.yaml
775
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/114321/meta.yaml: paired-uids
783
+ run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/263977/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/263977/meta.yaml
784
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/263977/meta.yaml: paired-uids
776
785
  caching parameters
777
786
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
778
787
  keeping 16 / 64 v genes
@@ -783,31 +792,31 @@ smith-waterman (new-allele fitting)
783
792
  kept 1 (0.027) unproductive
784
793
  water time: 0.2 (ig-sw 0.0 processing 0.2)
785
794
  smith-waterman (writing parameters)
786
- vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
795
+ vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.2 sec
787
796
  running 10 procs for 37 seqs
788
797
  info for 37 / 37 = 1.000 (removed: 0 failed)
789
798
  kept 1 (0.027) unproductive
790
799
  writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
791
- writing parameters to test/paired/new-results/test/parameters/data/igk/sw (2.3 sec)
792
- water time: 2.6 (ig-sw 2.4 processing 0.2)
800
+ writing parameters to test/paired/new-results/test/parameters/data/igk/sw (3.9 sec)
801
+ water time: 4.2 (ig-sw 4.0 processing 0.2)
793
802
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
794
803
 
795
804
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
796
- (1.8 sec)
805
+ (1.9 sec)
797
806
  hmm
798
807
  reading output
799
808
  read 37 hmm output lines with 37 sequences in 37 events (0 failures)
800
- writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (2.5 sec)
801
- infra time: 2.6
802
- hmm step time: 3.5
809
+ writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (3.5 sec)
810
+ infra time: 3.6
811
+ hmm step time: 4.5
803
812
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
804
813
 
805
814
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
806
- (1.8 sec)
807
- total time: 10.4
815
+ (2.1 sec)
816
+ total time: 13.5
808
817
  cache-parameters igl:
809
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/114321/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/114321/meta.yaml
810
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/114321/meta.yaml: paired-uids
818
+ run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/263977/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/263977/meta.yaml
819
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/263977/meta.yaml: paired-uids
811
820
  caching parameters
812
821
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.1 sec
813
822
  keeping 10 / 80 v genes
@@ -821,22 +830,22 @@ smith-waterman (writing parameters)
821
830
  running 10 procs for 15 seqs
822
831
  info for 15 / 15 = 1.000 (removed: 0 failed)
823
832
  writing sw results to test/paired/new-results/test/parameters/data/igl/sw-cache.yaml
824
- writing parameters to test/paired/new-results/test/parameters/data/igl/sw (1.5 sec)
825
- water time: 1.8 (ig-sw 1.6 processing 0.2)
833
+ writing parameters to test/paired/new-results/test/parameters/data/igl/sw (2.1 sec)
834
+ water time: 2.4 (ig-sw 2.2 processing 0.2)
826
835
  writing hmms removed 6 genes from glfo (leaving v 10 d 1 j 3)
827
836
 
828
837
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
829
- (1.2 sec)
838
+ (1.0 sec)
830
839
  hmm
831
840
  reading output
832
841
  read 15 hmm output lines with 15 sequences in 15 events (0 failures)
833
- writing parameters to test/paired/new-results/test/parameters/data/igl/hmm (1.3 sec)
834
- infra time: 1.4
835
- hmm step time: 1.9
842
+ writing parameters to test/paired/new-results/test/parameters/data/igl/hmm (1.9 sec)
843
+ infra time: 2.1
844
+ hmm step time: 2.5
836
845
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
837
846
 
838
847
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
839
848
  (1.0 sec)
840
- total time: 6.4
841
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/114321/: failed.fa
842
- total time: 42.4
849
+ total time: 7.6
850
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/263977/: failed.fa
851
+ total time: 53.9