partis-bcr 1.0.10__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11__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 (47) hide show
  1. bin/parse-output.py +2 -2
  2. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/parse-output.py +2 -2
  3. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/RECORD +47 -47
  5. test/new-results/test.log +9 -9
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  9. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +4 -4
  10. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
  11. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +3 -3
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  27. test/paired/new-results/run-times.csv +6 -6
  28. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +59 -59
  29. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +63 -64
  30. test/paired/new-results/subset-partition-new-simu/merged-partition.log +34 -34
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  34. test/paired/new-results/test.log +151 -151
  35. test/phylo-naive-run.py +1 -1
  36. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/cf-alleles.py +0 -0
  37. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/cf-germlines.py +0 -0
  38. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/compare-plotdirs.py +0 -0
  39. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/extract-pairing-info.py +0 -0
  40. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/gctree-run.py +0 -0
  41. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/get-naive-probabilities.py +0 -0
  42. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/partis-test.py +0 -0
  43. {partis_bcr-1.0.10.data → partis_bcr-1.0.11.data}/scripts/split-loci.py +0 -0
  44. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/WHEEL +0 -0
  45. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/entry_points.txt +0 -0
  46. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/licenses/COPYING +0 -0
  47. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.11.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -36,45 +36,45 @@ writing to paired subdirs
36
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  run partis cache-parameters --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
37
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  --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
38
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  caching parameters
39
- vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.1 sec
39
+ vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.0 sec
40
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  keeping 6 / 198 v genes
41
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  smith-waterman (new-allele fitting)
42
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  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
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  running 10 procs for 32 seqs
44
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  info for 32 / 32 = 1.000 (removed: 0 failed)
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  kept 14 (0.438) unproductive
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- water time: 0.2 (ig-sw 0.1 processing 0.1)
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+ water time: 0.2 (ig-sw 0.0 processing 0.1)
47
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  smith-waterman (writing parameters)
48
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  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
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  running 10 procs for 32 seqs
50
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  info for 32 / 32 = 1.000 (removed: 0 failed)
51
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  kept 14 (0.438) unproductive
52
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
53
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (2.2 sec)
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- water time: 2.5 (ig-sw 2.3 processing 0.2)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.9 sec)
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+ water time: 1.2 (ig-sw 1.1 processing 0.2)
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  writing hmms removed 18 genes from glfo (leaving v 6 d 16 j 4)
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57
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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- (1.0 sec)
58
+ (0.8 sec)
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  hmm
60
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  reading output
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  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
62
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (1.1 sec)
63
- infra time: 1.2
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- hmm step time: 2.0
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.9 sec)
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+ infra time: 1.0
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+ hmm step time: 1.7
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  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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- (0.8 sec)
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- total time: 7.1
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+ (0.7 sec)
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+ total time: 5.1
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  cache-parameters igk:
71
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  run partis cache-parameters --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
72
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  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
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  caching parameters
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- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
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  keeping 5 / 64 v genes
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  smith-waterman (new-allele fitting)
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- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
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  running 10 procs for 18 seqs
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  info for 18 / 18 = 1.000 (removed: 0 failed)
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  kept 9 (0.500) unproductive
@@ -85,8 +85,8 @@ smith-waterman (writing parameters)
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  info for 18 / 18 = 1.000 (removed: 0 failed)
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  kept 9 (0.500) unproductive
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
88
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (1.0 sec)
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- water time: 1.3 (ig-sw 1.1 processing 0.1)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.7 sec)
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+ water time: 1.0 (ig-sw 0.8 processing 0.2)
90
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  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
91
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -94,14 +94,14 @@ smith-waterman (writing parameters)
94
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  hmm
95
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  reading output
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  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.8 sec)
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- infra time: 1.0
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- hmm step time: 1.3
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.6 sec)
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+ infra time: 0.8
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+ hmm step time: 1.1
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  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
103
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  (0.5 sec)
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- total time: 4.2
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+ total time: 3.7
105
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  cache-parameters igl:
106
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  run partis cache-parameters --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
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  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -109,19 +109,19 @@ caching parameters
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  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
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  keeping 3 / 80 v genes
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  smith-waterman (new-allele fitting)
112
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
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+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
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  running 10 procs for 11 seqs
114
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  info for 11 / 11 = 1.000 (removed: 0 failed)
115
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  kept 7 (0.636) unproductive
116
- water time: 0.2 (ig-sw 0.0 processing 0.2)
116
+ water time: 0.1 (ig-sw 0.0 processing 0.1)
117
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  smith-waterman (writing parameters)
118
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
118
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
119
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  running 10 procs for 11 seqs
120
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  info for 11 / 11 = 1.000 (removed: 0 failed)
121
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  kept 7 (0.636) unproductive
122
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
123
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.6 sec)
124
- water time: 0.8 (ig-sw 0.7 processing 0.2)
123
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.4 sec)
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+ water time: 0.7 (ig-sw 0.5 processing 0.1)
125
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  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
126
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127
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -129,14 +129,14 @@ smith-waterman (writing parameters)
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  hmm
130
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  reading output
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  read 11 hmm output lines with 11 sequences in 11 events (0 failures)
132
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.5 sec)
133
- infra time: 0.6
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- hmm step time: 0.9
132
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.4 sec)
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+ infra time: 0.4
134
+ hmm step time: 0.8
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  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
136
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137
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
138
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  (0.3 sec)
139
- total time: 2.9
139
+ total time: 2.5
140
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  partition igh:
141
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  run partis partition --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
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  --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -148,20 +148,20 @@ smith-waterman
148
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  kept 14 (0.438) unproductive
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  water time: 0.0
150
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  hmm
151
- caching all 32 naive sequences (0.9s)
151
+ caching all 32 naive sequences (0.7s)
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  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
153
- 30 clusters with 10 procs (0.5s)
153
+ 30 clusters with 10 procs (0.4s)
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  29 clusters with 7 procs (0.4s)
155
- 28 clusters with 5 procs (0.5s)
155
+ 28 clusters with 5 procs (0.4s)
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  28 clusters with 3 procs (0.5s)
157
- 23 clusters with 2 procs (0.7s)
158
- 20 clusters with 1 proc (0.8s)
157
+ 23 clusters with 2 procs (0.5s)
158
+ 20 clusters with 1 proc (0.7s)
159
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  note not merging entire cpath history
160
- partition loop time: 3.5
160
+ partition loop time: 3.0
161
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  getting annotations for final partition
162
- subcluster annotating 16 clusters with steps: (0.6s) (0.3s)
163
- subcluster annotation time 0.9
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- total time: 5.6
162
+ subcluster annotating 16 clusters with steps: (0.5s) (0.3s)
163
+ subcluster annotation time 0.8
164
+ total time: 4.8
165
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  partition igk:
166
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  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
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  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -173,41 +173,41 @@ smith-waterman
173
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  kept 9 (0.500) unproductive
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  water time: 0.0
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  hmm
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- caching all 18 naive sequences (0.4s)
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+ caching all 18 naive sequences (0.3s)
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  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
178
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  reducing n procs to number of clusters: 10 --> 7
179
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  7 clusters with 7 procs (0.3s)
180
- 7 clusters with 5 procs (0.3s)
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- 7 clusters with 3 procs (0.3s)
182
- 6 clusters with 2 procs (0.1s)
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- 6 clusters with 1 proc (0.4s)
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- partition loop time: 1.4
180
+ 7 clusters with 5 procs (0.2s)
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+ 7 clusters with 3 procs (0.2s)
182
+ 6 clusters with 2 procs (0.2s)
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+ 6 clusters with 1 proc (0.3s)
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+ partition loop time: 1.2
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  getting annotations for final partition
186
- subcluster annotating 6 clusters with steps: (0.4s) (0.1s)
186
+ subcluster annotating 6 clusters with steps: (0.3s) (0.2s)
187
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  subcluster annotation time 0.5
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- total time: 2.4
188
+ total time: 2.1
189
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  partition igl:
190
190
  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
191
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  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
192
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  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
193
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  smith-waterman
194
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
194
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
195
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  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
196
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  info for 11 / 11 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
197
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  kept 7 (0.636) unproductive
198
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  water time: 0.0
199
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  hmm
200
- caching all 11 naive sequences (0.4s)
200
+ caching all 11 naive sequences (0.3s)
201
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  collapsed 11 queries into 3 clusters with identical naive seqs (0.0 sec)
202
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  reducing n procs to number of clusters: 10 --> 3
203
- 3 clusters with 3 procs (0.2s)
204
- 3 clusters with 2 procs (0.3s)
205
- 3 clusters with 1 proc (0.3s)
203
+ 3 clusters with 3 procs (0.3s)
204
+ 3 clusters with 2 procs (0.2s)
205
+ 3 clusters with 1 proc (0.2s)
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  partition loop time: 0.7
207
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  getting annotations for final partition
208
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  subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
209
- subcluster annotation time 0.4
210
- total time: 1.6
209
+ subcluster annotation time 0.3
210
+ total time: 1.4
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  combining chains
212
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  cleaning pair info for 61 seqs
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  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -227,24 +227,24 @@ cleaning pair info for 61 seqs
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  k 0 0 1
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  merge time 0.0
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  need to get annotations for 2/11 joint igh clusters
230
- tag: v1.0.10
230
+ tag: v1.0.11
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  annotate igh+igk: igh
232
232
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
233
233
  --input-metafnames: added meta info for 19 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml: loci paired-uids
234
234
  --input-partition-fname: read best partition with 19 sequences in 11 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
235
235
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
236
236
  smith-waterman
237
- vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.2 sec
237
+ vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.1 sec
238
238
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
239
239
  info for 19 / 19 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
240
240
  kept 7 (0.368) unproductive
241
241
  water time: 0.0
242
242
  hmm
243
- subcluster annotating 11 clusters with steps: (0.5s) (0.3s)
243
+ subcluster annotating 11 clusters with steps: (0.4s) (0.3s)
244
244
  subcluster annotation time 0.7
245
- total time: 0.9
245
+ total time: 0.8
246
246
  need to get annotations for 6/11 joint igk clusters
247
- tag: v1.0.10
247
+ tag: v1.0.11
248
248
  annotate igh+igk: igk
249
249
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
250
250
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml: loci paired-uids
@@ -259,9 +259,8 @@ smith-waterman
259
259
  hmm
260
260
  reading output
261
261
  read 11 hmm output lines with 18 sequences in 11 events (0 failures)
262
- infra time: 0.1
263
- hmm step time: 0.4
264
- total time: 0.5
262
+ hmm step time: 0.3
263
+ total time: 0.4
265
264
  igh+igl: synchronizing heavy and light chain cluster paths
266
265
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
267
266
  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
@@ -278,7 +277,7 @@ hmm
278
277
  l 0 0 1
279
278
  merge time 0.0
280
279
  need to get annotations for 2/5 joint igh clusters
281
- tag: v1.0.10
280
+ tag: v1.0.11
282
281
  annotate igh+igl: igh
283
282
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
284
283
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -293,16 +292,16 @@ smith-waterman
293
292
  hmm
294
293
  subcluster annotating 5 clusters with steps: (0.3s) (0.3s)
295
294
  subcluster annotation time 0.6
296
- total time: 0.8
295
+ total time: 0.7
297
296
  need to get annotations for 5/5 joint igl clusters
298
- tag: v1.0.10
297
+ tag: v1.0.11
299
298
  annotate igh+igl: igl
300
299
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
301
300
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
302
301
  --input-partition-fname: read best partition with 11 sequences in 5 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
303
302
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
304
303
  smith-waterman
305
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
304
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
306
305
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
307
306
  info for 11 / 11 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
308
307
  kept 7 (0.636) unproductive
@@ -323,4 +322,4 @@ hmm
323
322
  h 16 --> 16
324
323
  k 6 --> 11 +5
325
324
  l 3 --> 5 +2
326
- total time: 54.2
325
+ total time: 44.1
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -28,15 +28,15 @@ hmm
28
28
  --continue-from-input-partition: using input partition for initial cpath
29
29
  27 clusters (53 seqs)
30
30
  27 clusters with 10 procs (0.6s)
31
- 26 clusters with 7 procs (0.6s)
32
- 23 clusters with 5 procs (0.5s)
31
+ 26 clusters with 7 procs (0.5s)
32
+ 23 clusters with 5 procs (0.4s)
33
33
  22 clusters with 3 procs (0.5s)
34
34
  21 clusters with 2 procs (0.4s)
35
- 21 clusters with 1 proc (0.9s)
36
- partition loop time: 3.5
35
+ 21 clusters with 1 proc (0.8s)
36
+ partition loop time: 3.3
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (0.8s) (0.4s) (0.3s)
39
- subcluster annotation time 1.5
38
+ subcluster annotating 18 clusters with steps: (0.7s) (0.4s) (0.3s)
39
+ subcluster annotation time 1.4
40
40
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
41
41
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
42
42
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
@@ -47,7 +47,7 @@ getting annotations for final partition
47
47
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
48
48
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
49
49
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
50
- total time: 5.3
50
+ total time: 5.1
51
51
  partition igk:
52
52
  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igk.yaml --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
53
53
  warning replacing 'paired-uids'/'paired-uids' value for 'bc11af4843-igk' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['bc11af4843-igh', 'eee6809ad6-igh', 'eee6809ad6-igl'] --> ['eee6809ad6-igh']
@@ -77,14 +77,14 @@ hmm
77
77
  17 clusters with 7 procs (0.3s)
78
78
  15 clusters with 5 procs (0.3s)
79
79
  12 clusters with 3 procs (0.2s)
80
- 11 clusters with 2 procs (0.3s)
80
+ 11 clusters with 2 procs (0.2s)
81
81
  7 clusters with 1 proc (0.4s)
82
82
  note not merging entire cpath history
83
- partition loop time: 1.8
83
+ partition loop time: 1.7
84
84
  getting annotations for final partition
85
- subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.2s)
86
- subcluster annotation time 1.0
87
- total time: 3.1
85
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.2s)
86
+ subcluster annotation time 0.9
87
+ total time: 2.6
88
88
  partition igl:
89
89
  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igl.yaml --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
90
90
  warning replacing 'paired-uids'/'paired-uids' value for '7588f09c07-igl' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['7588f09c07-igh', 'cb8a759f1a-igh'] --> ['7588f09c07-igh']
@@ -102,7 +102,7 @@ getting annotations for final partition
102
102
  removed 3/21 queries from input info that were absent from input partition
103
103
  partitioning (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm)
104
104
  smith-waterman
105
- vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.2 sec
105
+ vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.1 sec
106
106
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
107
107
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
108
108
  kept 13 (0.722) unproductive
@@ -119,17 +119,17 @@ hmm
119
119
  6 clusters with 3 procs (0.2s)
120
120
  6 clusters with 2 procs (0.2s)
121
121
  3 clusters with 1 proc (0.3s)
122
- partition loop time: 1.5
122
+ partition loop time: 1.4
123
123
  getting annotations for final partition
124
- subcluster annotating 3 clusters with steps: (0.3s) (0.1s) (0.2s)
125
- subcluster annotation time 0.6
124
+ subcluster annotating 3 clusters with steps: (0.3s) (0.2s) (0.2s)
125
+ subcluster annotation time 0.7
126
126
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
127
127
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
128
128
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
129
129
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
130
130
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
131
131
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
132
- total time: 2.4
132
+ total time: 2.2
133
133
  combining chains
134
134
  cleaning pair info for 107 seqs
135
135
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -165,7 +165,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
165
165
  joint 0.963 0.594
166
166
  merge time 0.0
167
167
  need to get annotations for 6/15 joint igh clusters
168
- tag: v1.0.10
168
+ tag: v1.0.11
169
169
  annotate igh+igk: igh
170
170
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
171
171
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -179,11 +179,11 @@ smith-waterman
179
179
  kept 13 (0.371) unproductive
180
180
  water time: 0.0
181
181
  hmm
182
- subcluster annotating 15 clusters with steps: (0.7s) (0.3s)
183
- subcluster annotation time 1.0
184
- total time: 1.1
182
+ subcluster annotating 15 clusters with steps: (0.6s) (0.3s)
183
+ subcluster annotation time 0.8
184
+ total time: 1.0
185
185
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.10
186
+ tag: v1.0.11
187
187
  annotate igh+igk: igk
188
188
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
189
189
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -191,14 +191,14 @@ hmm
191
191
  --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml
192
192
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm)
193
193
  smith-waterman
194
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
194
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
195
195
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
196
196
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
197
197
  kept 14 (0.389) unproductive
198
198
  water time: 0.0
199
199
  hmm
200
- subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
201
- subcluster annotation time 0.7
200
+ subcluster annotating 15 clusters with steps: (0.5s) (0.1s)
201
+ subcluster annotation time 0.6
202
202
  total time: 0.9
203
203
  igh+igl: synchronizing heavy and light chain cluster paths
204
204
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
@@ -228,7 +228,7 @@ hmm
228
228
  joint 1.000 0.787
229
229
  merge time 0.0
230
230
  need to get annotations for 2/6 joint igh clusters
231
- tag: v1.0.10
231
+ tag: v1.0.11
232
232
  annotate igh+igl: igh
233
233
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
234
234
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -236,17 +236,17 @@ hmm
236
236
  --input-partition-fname: read best partition with 19 sequences in 6 clusters from test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml
237
237
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
238
238
  smith-waterman
239
- vsearch: 19 / 19 v annotations (0 failed) with 4 v genes in 0.1 sec
239
+ vsearch: 19 / 19 v annotations (0 failed) with 4 v genes in 0.2 sec
240
240
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
241
241
  info for 19 / 19 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
242
242
  kept 11 (0.579) unproductive
243
243
  water time: 0.0
244
244
  hmm
245
- subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.3s)
246
- subcluster annotation time 1.1
245
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.3s)
246
+ subcluster annotation time 1.0
247
247
  total time: 1.2
248
248
  need to get annotations for 6/6 joint igl clusters
249
- tag: v1.0.10
249
+ tag: v1.0.11
250
250
  annotate igh+igl: igl
251
251
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
252
252
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igl.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml --ignore-sw-pair-info
@@ -254,14 +254,14 @@ hmm
254
254
  --input-partition-fname: read best partition with 18 sequences in 6 clusters from test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml
255
255
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm)
256
256
  smith-waterman
257
- vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.1 sec
257
+ vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.2 sec
258
258
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
259
259
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
260
260
  kept 13 (0.722) unproductive
261
261
  water time: 0.0
262
262
  hmm
263
- subcluster annotating 6 clusters with steps: (0.3s) (0.2s) (0.2s)
264
- subcluster annotation time 0.7
263
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.1s)
264
+ subcluster annotation time 0.6
265
265
  total time: 0.8
266
266
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml
267
267
  concatenating heavy chain loci:
@@ -276,4 +276,4 @@ hmm
276
276
  h 18 --> 21 +3
277
277
  k 6 --> 15 +9
278
278
  l 3 --> 6 +3
279
- total time: 33.3
279
+ total time: 27.9