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/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 0.2 sec
8
+ vsearch: 56 / 56 v annotations (0 failed) with 9 v genes in 0.1 sec
9
9
  keeping 6 / 198 v genes
10
10
  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
11
  smith-waterman (new-allele fitting)
@@ -15,39 +15,39 @@ smith-waterman (new-allele fitting)
15
15
  kept 25 (0.446) unproductive
16
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  water time: 0.2 (ig-sw 0.1 processing 0.1)
17
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  smith-waterman (writing parameters)
18
- vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.2 sec
18
+ vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.1 sec
19
19
  running 10 procs for 56 seqs
20
20
  info for 56 / 56 = 1.000 (removed: 0 failed)
21
21
  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 (1.1 sec)
24
- water time: 1.5 (ig-sw 1.3 processing 0.2)
23
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.8 sec)
24
+ water time: 1.1 (ig-sw 1.0 processing 0.1)
25
25
  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
26
26
 
27
27
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
28
- (0.9 sec)
28
+ (0.7 sec)
29
29
  hmm
30
30
  reading output
31
31
  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 (1.0 sec)
33
- writing parameters to test/paired/new-results/test/parameters/simu/igh/true (1.0 sec)
34
- infra time: 2.2
35
- hmm step time: 3.3
32
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.7 sec)
33
+ writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.7 sec)
34
+ infra time: 1.5
35
+ hmm step time: 2.5
36
36
  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
- (0.8 sec)
40
- total time: 7.3
39
+ (0.6 sec)
40
+ total time: 5.5
41
41
  cache-parameters igk:
42
42
  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 0.2 sec
46
+ vsearch: 36 / 36 v annotations (0 failed) with 6 v genes in 0.1 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 0.2 sec
50
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
51
51
  running 10 procs for 36 seqs
52
52
  running 11 procs for 2 seqs
53
53
  info for 36 / 36 = 1.000 (removed: 0 failed)
@@ -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 (0.8 sec)
64
- water time: 1.2 (ig-sw 0.9 processing 0.1)
63
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/sw (0.6 sec)
64
+ water time: 1.0 (ig-sw 0.7 processing 0.1)
65
65
  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
66
66
 
67
67
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
68
- (0.5 sec)
68
+ (0.4 sec)
69
69
  hmm
70
70
  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)
73
- writing parameters to test/paired/new-results/test/parameters/simu/igk/true (1.0 sec)
74
- infra time: 2.1
75
- hmm step time: 2.7
72
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.6 sec)
73
+ writing parameters to test/paired/new-results/test/parameters/simu/igk/true (0.6 sec)
74
+ infra time: 1.4
75
+ hmm step time: 1.8
76
76
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
77
77
 
78
78
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
79
- (0.6 sec)
80
- total time: 6.1
79
+ (0.4 sec)
80
+ total time: 4.3
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
@@ -87,36 +87,36 @@ caching parameters
87
87
  keeping 3 / 80 v genes
88
88
  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
89
  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
91
  running 10 procs for 21 seqs
92
92
  info for 21 / 21 = 1.000 (removed: 0 failed)
93
93
  kept 14 (0.667) unproductive
94
- water time: 0.2 (ig-sw 0.0 processing 0.1)
94
+ water time: 0.1 (ig-sw 0.0 processing 0.1)
95
95
  smith-waterman (writing parameters)
96
96
  vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.1 sec
97
97
  running 10 procs for 21 seqs
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 (1.1 sec)
102
- water time: 1.4 (ig-sw 1.2 processing 0.2)
101
+ writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.4 sec)
102
+ water time: 0.6 (ig-sw 0.5 processing 0.1)
103
103
  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
106
- (0.8 sec)
106
+ (0.3 sec)
107
107
  hmm
108
108
  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 (0.6 sec)
111
- writing parameters to test/paired/new-results/test/parameters/simu/igl/true (0.4 sec)
112
- infra time: 1.2
113
- hmm step time: 2.9
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 (0.3 sec)
112
+ infra time: 0.8
113
+ hmm step time: 1.2
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: 6.0
119
- total time: 28.6
117
+ (0.2 sec)
118
+ total time: 2.8
119
+ total time: 18.1
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
122
  partition igh:
@@ -125,39 +125,39 @@ hmm
125
125
  --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
127
  smith-waterman
128
- vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.2 sec
128
+ vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.1 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
132
132
  plotting performance
133
133
  warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
134
134
  (0.0 sec)
135
- water time: 0.2
135
+ water time: 0.1
136
136
  hmm
137
- caching all 56 naive sequences (1.5s)
137
+ caching all 56 naive sequences (0.9s)
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 (1.2s)
141
- 36 clusters with 5 procs (0.9s)
142
- 31 clusters with 3 procs (0.6s)
143
- 29 clusters with 2 procs (1.0s)
144
- 23 clusters with 1 proc (1.4s)
139
+ 50 clusters with 10 procs (0.7s)
140
+ 44 clusters with 7 procs (0.7s)
141
+ 36 clusters with 5 procs (0.6s)
142
+ 31 clusters with 3 procs (0.4s)
143
+ 29 clusters with 2 procs (0.7s)
144
+ 23 clusters with 1 proc (0.8s)
145
145
  note not merging entire cpath history
146
- partition loop time: 6.2
146
+ partition loop time: 4.0
147
147
  getting annotations for final partition
148
- subcluster annotating 20 clusters with steps: (0.9s) (0.4s) plotting performance
148
+ subcluster annotating 20 clusters with steps: (0.7s) (0.3s) 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
- subcluster annotation time 1.4
153
- total time: 9.6
152
+ subcluster annotation time 1.1
153
+ total time: 6.4
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
@@ -168,30 +168,30 @@ hmm
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 (0.2s)
172
- 7 clusters with 3 procs (0.3s)
173
- 7 clusters with 2 procs (0.3s)
174
- 6 clusters with 1 proc (0.4s)
175
- partition loop time: 1.6
171
+ 7 clusters with 5 procs (0.3s)
172
+ 7 clusters with 3 procs (0.2s)
173
+ 7 clusters with 2 procs (0.2s)
174
+ 6 clusters with 1 proc (0.3s)
175
+ partition loop time: 1.4
176
176
  getting annotations for final partition
177
- subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.2s) plotting performance (0.0 sec)
177
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.3s) plotting performance (0.0 sec)
178
178
 
179
- subcluster annotation time 1.0
180
- total time: 3.4
179
+ subcluster annotation time 0.9
180
+ total time: 3.2
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
184
184
  --input-metafnames: added meta info for 21 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
185
185
  partitioning (with test/paired/new-results/test/parameters/simu/igl/hmm)
186
186
  smith-waterman
187
- vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.1 sec
187
+ vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.2 sec
188
188
  reading sw results from test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
189
189
  info for 21 / 21 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
190
190
  kept 14 (0.667) unproductive
191
191
  plotting performance (0.0 sec)
192
192
  water time: 0.1
193
193
  hmm
194
- caching all 21 naive sequences (0.5s)
194
+ caching all 21 naive sequences (0.4s)
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
197
  3 clusters with 3 procs (0.2s)
@@ -199,10 +199,10 @@ hmm
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: (0.3s) (0.2s) (0.1s) plotting performance (0.0 sec)
202
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s) (0.1s) plotting performance (0.0 sec)
203
203
 
204
- subcluster annotation time 0.7
205
- total time: 2.1
204
+ subcluster annotation time 0.6
205
+ total time: 2.0
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
@@ -253,9 +253,9 @@ smith-waterman
253
253
  kept 13 (0.361) unproductive
254
254
  water time: 0.0
255
255
  hmm
256
- subcluster annotating 15 clusters with steps: (0.7s) (0.2s)
257
- subcluster annotation time 0.9
258
- total time: 1.1
256
+ subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
257
+ subcluster annotation time 0.8
258
+ total time: 0.9
259
259
  need to get annotations for 13/15 joint igk clusters
260
260
  annotate igh+igk: igk
261
261
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -264,15 +264,15 @@ hmm
264
264
  --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
265
265
  annotating (with test/paired/new-results/test/parameters/simu/igk/hmm)
266
266
  smith-waterman
267
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
267
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
268
268
  reading sw results from test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
269
269
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
270
270
  kept 14 (0.389) unproductive
271
271
  water time: 0.0
272
272
  hmm
273
- subcluster annotating 15 clusters with steps: (0.6s) (0.2s)
274
- subcluster annotation time 0.8
275
- total time: 1.0
273
+ subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
274
+ subcluster annotation time 0.6
275
+ total time: 0.8
276
276
  igh+igl: synchronizing heavy and light chain cluster paths
277
277
  removing badly + unpaired seqs: kept 7 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 3 l 4
278
278
  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
@@ -305,15 +305,15 @@ hmm
305
305
  --input-partition-fname: read best partition with 20 sequences in 8 clusters from test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
306
306
  annotating (with test/paired/new-results/test/parameters/simu/igh/hmm)
307
307
  smith-waterman
308
- vsearch: 20 / 20 v annotations (0 failed) with 4 v genes in 0.2 sec
308
+ vsearch: 20 / 20 v annotations (0 failed) with 4 v genes in 0.1 sec
309
309
  reading sw results from test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
310
310
  info for 20 / 20 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
311
311
  kept 12 (0.600) unproductive
312
312
  water time: 0.0
313
313
  hmm
314
- subcluster annotating 8 clusters with steps: (0.5s) (0.3s)
315
- subcluster annotation time 0.8
316
- total time: 1.0
314
+ subcluster annotating 8 clusters with steps: (0.4s) (0.3s)
315
+ subcluster annotation time 0.7
316
+ total time: 0.8
317
317
  need to get annotations for 8/8 joint igl clusters
318
318
  annotate igh+igl: igl
319
319
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -328,9 +328,9 @@ smith-waterman
328
328
  kept 14 (0.667) unproductive
329
329
  water time: 0.0
330
330
  hmm
331
- subcluster annotating 8 clusters with steps: (0.4s) (0.2s)
332
- subcluster annotation time 0.6
333
- total time: 0.8
331
+ subcluster annotating 8 clusters with steps: (0.3s) (0.2s)
332
+ subcluster annotation time 0.5
333
+ total time: 0.6
334
334
  concatenating heavy chain loci:
335
335
  h starting with 15 annotations (36 seqs)
336
336
  k starting with 15 annotations (36 seqs)
@@ -343,7 +343,7 @@ hmm
343
343
  h 20 --> 23 +3
344
344
  k 6 --> 15 +9
345
345
  l 3 --> 8 +5
346
- total time: 38.7
346
+ total time: 30.3
347
347
  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
348
  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
349
349
  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -374,7 +374,7 @@ hmm
374
374
  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
375
375
  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
376
  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
377
- total time: 168.4
377
+ total time: 113.1
378
378
  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
379
  removing seqs very different from seed seq
380
380
  wrong/no removed singly kept missing
@@ -399,33 +399,33 @@ smith-waterman
399
399
  kept 8 (0.471) unproductive
400
400
  water time: 0.0
401
401
  hmm
402
- caching all 17 naive sequences (0.6s)
402
+ caching all 17 naive sequences (0.4s)
403
403
  collapsed 17 queries into 17 clusters with identical naive seqs (0.0 sec)
404
404
  17 clusters with 10 procs (0.4s)
405
405
  17 clusters with 7 procs (0.4s)
406
406
  17 clusters with 5 procs (0.4s)
407
- 17 clusters with 3 procs (0.4s)
408
- 14 clusters with 2 procs (0.4s)
409
- 14 clusters with 1 proc (0.6s)
410
- partition loop time: 2.7
407
+ 17 clusters with 3 procs (0.3s)
408
+ 14 clusters with 2 procs (0.3s)
409
+ 14 clusters with 1 proc (0.5s)
410
+ partition loop time: 2.3
411
411
  getting annotations for final partition
412
412
  reading output
413
413
  read 12 hmm output lines with 17 sequences in 12 events (0 failures)
414
- hmm step time: 0.5
415
- total time: 3.8
414
+ hmm step time: 0.4
415
+ total time: 3.3
416
416
  partition igk:
417
417
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
418
418
  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
419
  --input-metafnames: added meta info for 12 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
420
420
  partitioning (with test/paired/new-results/test/parameters/simu/igk/hmm)
421
421
  smith-waterman
422
- vsearch: 12 / 12 v annotations (0 failed) with 2 v genes in 0.1 sec
422
+ vsearch: 12 / 12 v annotations (0 failed) with 2 v genes in 0.2 sec
423
423
  reading sw results from test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
424
424
  info for 12 / 12 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
425
425
  kept 7 (0.583) unproductive
426
426
  water time: 0.0
427
427
  hmm
428
- caching all 12 naive sequences (0.4s)
428
+ caching all 12 naive sequences (0.3s)
429
429
  collapsed 12 queries into 3 clusters with identical naive seqs (0.0 sec)
430
430
  reducing n procs to number of clusters: 10 --> 3
431
431
  3 clusters with 3 procs (0.2s)
@@ -433,9 +433,9 @@ hmm
433
433
  3 clusters with 1 proc (0.2s)
434
434
  partition loop time: 0.6
435
435
  getting annotations for final partition
436
- subcluster annotating 2 clusters with steps: (0.3s) (0.2s) (0.2s)
437
- subcluster annotation time 0.7
438
- total time: 1.8
436
+ subcluster annotating 2 clusters with steps: (0.2s) (0.2s) (0.2s)
437
+ subcluster annotation time 0.6
438
+ total time: 1.7
439
439
  partition igl:
440
440
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
441
441
  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
@@ -448,17 +448,17 @@ smith-waterman
448
448
  info for 4 / 4 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
449
449
  water time: 0.0
450
450
  hmm
451
- caching all 4 naive sequences (0.3s)
451
+ caching all 4 naive sequences (0.2s)
452
452
  collapsed 4 queries into 2 clusters with identical naive seqs (0.0 sec)
453
453
  reducing n procs to number of clusters: 4 --> 2
454
454
  2 clusters with 2 procs (0.2s)
455
- 2 clusters with 1 proc (0.2s)
455
+ 2 clusters with 1 proc (0.1s)
456
456
  partition loop time: 0.4
457
457
  getting annotations for final partition
458
458
  reading output
459
459
  read 2 hmm output lines with 4 sequences in 2 events (0 failures)
460
460
  hmm step time: 0.2
461
- total time: 1.0
461
+ total time: 0.8
462
462
  combining chains
463
463
  cleaning pair info for 33 seqs
464
464
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -514,7 +514,7 @@ hmm
514
514
  reading output
515
515
  read 1 hmm output lines with 1 sequences in 1 events (0 failures)
516
516
  hmm step time: 0.2
517
- total time: 0.4
517
+ total time: 0.3
518
518
  removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
519
519
  need to get annotations for 1/1 joint igk clusters
520
520
  seed cluster size in best joint partition: 1, excluding seed seq: 0
@@ -536,7 +536,7 @@ hmm
536
536
  reading output
537
537
  read 1 hmm output lines with 1 sequences in 1 events (0 failures)
538
538
  hmm step time: 0.1
539
- total time: 0.3
539
+ total time: 0.2
540
540
  igh+igl: synchronizing heavy and light chain cluster paths
541
541
  removing badly + unpaired seqs: kept 1 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 1 l 0
542
542
  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
@@ -564,7 +564,7 @@ hmm
564
564
  N clusters with all seqs:
565
565
  h 12 --> 1 -11
566
566
  k 2 --> 1 -1
567
- total time: 22.6
567
+ total time: 15.9
568
568
  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
569
  get-selection-metrics igh+igk: igh
570
570
  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 +577,7 @@ hmm
577
577
  starting 2 jobs
578
578
  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
579
  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 (0.3s)
580
+ made 2 fasttree trees (0.2s)
581
581
  tree origins: 2 ran fasttree
582
582
  skipped 3/5 clusters smaller than 4
583
583
  setting default tau to 1 / 385 = 0.0026
@@ -588,7 +588,7 @@ hmm
588
588
  warning get_aa_tree() (AA inf tree, iclust 1): skipped 9/11 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: eov flx ily npq
589
589
  skipped 3/5 clusters that had no uids in common with tree
590
590
  writing selection metrics to test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml
591
- total time: 0.4
591
+ total time: 0.3
592
592
  get-selection-metrics igh+igk: igk
593
593
  run partis get-selection-metrics --locus igk --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-igk.yaml
594
594
  note: --parameter-dir not set, so using default: x-dummy-x
@@ -600,7 +600,7 @@ hmm
600
600
  starting 2 jobs
601
601
  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-igk/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa
602
602
  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-igk/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa
603
- made 2 fasttree trees (0.3s)
603
+ made 2 fasttree trees (0.2s)
604
604
  tree origins: 2 ran fasttree
605
605
  skipped 2/4 clusters smaller than 4
606
606
  setting default tau to 1 / 337 = 0.0030
@@ -611,7 +611,7 @@ hmm
611
611
  warning get_aa_tree() (AA inf tree, iclust 1): skipped 2/9 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: eov
612
612
  skipped 2/4 clusters that had no uids in common with tree
613
613
  writing selection metrics to test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml
614
- total time: 0.4
614
+ total time: 0.3
615
615
  get-selection-metrics igh+igl: igh
616
616
  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+igl/partition-igh.yaml
617
617
  note: --parameter-dir not set, so using default: x-dummy-x
@@ -685,10 +685,10 @@ hmm
685
685
  skipped 1/4 clusters that had no uids in common with tree
686
686
  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
687
687
  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
688
- total time: 13.0
688
+ total time: 9.1
689
689
  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
690
  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/689194/meta.yaml --n-max-queries 100
691
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/694350/meta.yaml --n-max-queries 100
692
692
  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
693
693
  extract_pairing_info(): read 100 sequences with 48 droplet ids
694
694
  droplet id separators (set automatically): _ indices: [0]
@@ -699,14 +699,14 @@ hmm
699
699
  2 42 0.875
700
700
  3 2 0.042
701
701
  4 2 0.042
702
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/689194 --input-metafname /tmp/runner/hmms/689194/meta.yaml --n-max-queries 100
702
+ run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/694350 --input-metafname /tmp/runner/hmms/694350/meta.yaml --n-max-queries 100
703
703
  --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/689194/meta.yaml: paired-uids
704
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/694350/meta.yaml: paired-uids
705
705
  read pairing info for 100 seqs from input meta file
706
706
  running vsearch on 100 sequences:
707
- igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.2 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 0.2 sec
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 0.2 sec
709
+ igl: 15 / 100 v annotations (85 failed) with 12 v genes in 0.1 sec
710
710
  totals: igh 48 igk 37 igl 15
711
711
  count frac paired with
712
712
  h 31 0.65 k
@@ -724,10 +724,10 @@ totals: igh 48 igk 37 igl 15
724
724
  2 0.13 h l
725
725
  1 0.07 h k
726
726
  1 0.07 h h k
727
- writing to /tmp/runner/hmms/689194/
728
- igh: 48 to 689194/igh.fa
729
- igk: 37 to 689194/igk.fa
730
- igl: 15 to 689194/igl.fa
727
+ writing to /tmp/runner/hmms/694350/
728
+ igh: 48 to 694350/igh.fa
729
+ igk: 37 to 694350/igk.fa
730
+ igl: 15 to 694350/igl.fa
731
731
  writing to paired subdirs
732
732
  igh+igk:
733
733
  igh: 36 / 48 to igh+igk/igh.fa
@@ -736,45 +736,45 @@ writing to paired subdirs
736
736
  igh: 15 / 48 to igh+igl/igh.fa
737
737
  igl: 15 / 15 to igh+igl/igl.fa
738
738
  cache-parameters igh:
739
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/689194/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/689194/meta.yaml
740
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/689194/meta.yaml: paired-uids
739
+ run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/694350/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/694350/meta.yaml
740
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/694350/meta.yaml: paired-uids
741
741
  caching parameters
742
742
  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.1 sec
743
743
  keeping 23 / 198 v genes
744
744
  smith-waterman (new-allele fitting)
745
- vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.2 sec
745
+ vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.1 sec
746
746
  running 10 procs for 48 seqs
747
747
  info for 48 / 48 = 1.000 (removed: 0 failed)
748
748
  kept 1 (0.021) unproductive
749
749
  water time: 0.2 (ig-sw 0.0 processing 0.2)
750
750
  smith-waterman (writing parameters)
751
- vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.2 sec
751
+ vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.1 sec
752
752
  running 10 procs for 48 seqs
753
753
  info for 48 / 48 = 1.000 (removed: 0 failed)
754
754
  kept 1 (0.021) unproductive
755
755
  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 (3.7 sec)
757
- water time: 4.0 (ig-sw 3.8 processing 0.2)
756
+ writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.7 sec)
757
+ water time: 3.1 (ig-sw 2.9 processing 0.2)
758
758
  writing hmms removed 13 genes from glfo (leaving v 23 d 19 j 6)
759
759
 
760
760
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
761
- (2.4 sec)
761
+ (1.9 sec)
762
762
  hmm
763
763
  reading output
764
764
  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 (4.0 sec)
766
- infra time: 4.2
767
- hmm step time: 5.4
765
+ writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (2.8 sec)
766
+ infra time: 3.0
767
+ hmm step time: 3.9
768
768
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
769
769
 
770
770
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
771
- (2.6 sec)
772
- total time: 15.4
771
+ (1.9 sec)
772
+ total time: 11.6
773
773
  cache-parameters igk:
774
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/689194/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/689194/meta.yaml
775
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/689194/meta.yaml: paired-uids
774
+ run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/694350/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/694350/meta.yaml
775
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/694350/meta.yaml: paired-uids
776
776
  caching parameters
777
- vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.2 sec
777
+ vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
778
778
  keeping 16 / 64 v genes
779
779
  smith-waterman (new-allele fitting)
780
780
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
@@ -783,60 +783,60 @@ smith-waterman (new-allele fitting)
783
783
  kept 1 (0.027) unproductive
784
784
  water time: 0.2 (ig-sw 0.0 processing 0.2)
785
785
  smith-waterman (writing parameters)
786
- vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.2 sec
786
+ vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
787
787
  running 10 procs for 37 seqs
788
788
  info for 37 / 37 = 1.000 (removed: 0 failed)
789
789
  kept 1 (0.027) unproductive
790
790
  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 (3.8 sec)
792
- water time: 4.2 (ig-sw 4.0 processing 0.2)
791
+ writing parameters to test/paired/new-results/test/parameters/data/igk/sw (2.0 sec)
792
+ water time: 2.3 (ig-sw 2.1 processing 0.2)
793
793
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
794
794
 
795
795
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
796
- (2.1 sec)
796
+ (1.2 sec)
797
797
  hmm
798
798
  reading output
799
799
  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 (3.3 sec)
801
- infra time: 3.5
802
- hmm step time: 4.3
800
+ writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (2.0 sec)
801
+ infra time: 2.1
802
+ hmm step time: 2.6
803
803
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
804
804
 
805
805
  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: 13.4
806
+ (1.2 sec)
807
+ total time: 8.0
808
808
  cache-parameters igl:
809
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/689194/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/689194/meta.yaml
810
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/689194/meta.yaml: paired-uids
809
+ run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/694350/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/694350/meta.yaml
810
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/694350/meta.yaml: paired-uids
811
811
  caching parameters
812
812
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.1 sec
813
813
  keeping 10 / 80 v genes
814
814
  smith-waterman (new-allele fitting)
815
- vsearch: 15 / 15 v annotations (0 failed) with 10 v genes in 0.1 sec
815
+ vsearch: 15 / 15 v annotations (0 failed) with 10 v genes in 0.0 sec
816
816
  running 10 procs for 15 seqs
817
817
  info for 15 / 15 = 1.000 (removed: 0 failed)
818
- water time: 0.2 (ig-sw 0.0 processing 0.2)
818
+ water time: 0.2 (ig-sw 0.0 processing 0.1)
819
819
  smith-waterman (writing parameters)
820
820
  vsearch: 15 / 15 v annotations (0 failed) with 10 v genes in 0.2 sec
821
821
  running 10 procs for 15 seqs
822
822
  info for 15 / 15 = 1.000 (removed: 0 failed)
823
823
  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 (2.4 sec)
825
- water time: 2.7 (ig-sw 2.5 processing 0.2)
824
+ writing parameters to test/paired/new-results/test/parameters/data/igl/sw (1.2 sec)
825
+ water time: 1.5 (ig-sw 1.3 processing 0.2)
826
826
  writing hmms removed 6 genes from glfo (leaving v 10 d 1 j 3)
827
827
 
828
828
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
829
- (1.1 sec)
829
+ (0.8 sec)
830
830
  hmm
831
831
  reading output
832
832
  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 (2.0 sec)
834
- infra time: 2.2
835
- hmm step time: 2.6
833
+ writing parameters to test/paired/new-results/test/parameters/data/igl/hmm (1.2 sec)
834
+ infra time: 1.2
835
+ hmm step time: 1.6
836
836
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
837
837
 
838
838
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
839
- (1.5 sec)
840
- total time: 8.6
841
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/689194/: failed.fa
842
- total time: 49.1
839
+ (0.7 sec)
840
+ total time: 5.1
841
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/694350/: failed.fa
842
+ total time: 32.5