partis-bcr 1.0.12.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (64) hide show
  1. packages/bpp/lib/libbpp-core.a +0 -0
  2. packages/bpp/lib/libbpp-core.so +0 -0
  3. packages/bpp/lib/libbpp-core.so.2 +0 -0
  4. packages/bpp/lib/libbpp-core.so.2.0.3 +0 -0
  5. packages/bpp/lib/libbpp-phyl.a +0 -0
  6. packages/bpp/lib/libbpp-phyl.so +0 -0
  7. packages/bpp/lib/libbpp-phyl.so.9 +0 -0
  8. packages/bpp/lib/libbpp-phyl.so.9.1.3 +0 -0
  9. packages/bpp/lib/libbpp-seq.a +0 -0
  10. packages/bpp/lib/libbpp-seq.so +0 -0
  11. packages/bpp/lib/libbpp-seq.so.9 +0 -0
  12. packages/bpp/lib/libbpp-seq.so.9.1.3 +0 -0
  13. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/METADATA +1 -1
  14. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/RECORD +64 -52
  15. test/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  16. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  17. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  18. test/new-results/run-times.csv +8 -8
  19. test/new-results/test.log +50 -50
  20. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  21. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  22. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  23. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +3 -3
  24. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +4 -4
  25. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +1 -1
  26. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +1 -1
  27. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +4 -4
  28. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +5 -5
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  37. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  38. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  39. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  40. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  41. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  42. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  43. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  44. test/paired/new-results/run-times.csv +6 -6
  45. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +71 -67
  46. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +71 -66
  47. test/paired/new-results/subset-partition-new-simu/merged-partition.log +43 -39
  48. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  49. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  50. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  51. test/paired/new-results/test.log +166 -157
  52. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/cf-alleles.py +0 -0
  53. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/cf-germlines.py +0 -0
  54. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/compare-plotdirs.py +0 -0
  55. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/extract-pairing-info.py +0 -0
  56. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/gctree-run.py +0 -0
  57. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/get-naive-probabilities.py +0 -0
  58. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/parse-output.py +0 -0
  59. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/partis-test.py +0 -0
  60. {partis_bcr-1.0.12.post1.dev3.data → partis_bcr-1.0.13.data}/scripts/split-loci.py +0 -0
  61. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/WHEEL +0 -0
  62. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/entry_points.txt +0 -0
  63. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/licenses/COPYING +0 -0
  64. {partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -36,72 +36,72 @@ writing to paired subdirs
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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
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  caching parameters
39
- vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.1 sec
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+ vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.2 sec
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  keeping 6 / 198 v genes
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  smith-waterman (new-allele fitting)
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- vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
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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
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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: 0.1 (ig-sw 0.0 processing 0.1)
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+ water time: 0.2 (ig-sw 0.0 processing 0.2)
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  smith-waterman (writing parameters)
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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
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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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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.8 sec)
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- water time: 1.0 (ig-sw 0.9 processing 0.1)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (1.3 sec)
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+ water time: 1.6 (ig-sw 1.5 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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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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- (0.7 sec)
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+ (1.0 sec)
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  hmm
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  reading output
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  read 32 hmm output lines with 32 sequences in 32 events (0 failures)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.7 sec)
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- infra time: 0.8
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- hmm step time: 1.4
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (1.1 sec)
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+ infra time: 1.2
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+ hmm step time: 2.1
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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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- (0.6 sec)
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- total time: 4.4
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+ (0.9 sec)
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+ total time: 6.5
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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
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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
74
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 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 0.0 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
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- water time: 0.1 (ig-sw 0.0 processing 0.1)
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+ water time: 0.2 (ig-sw 0.0 processing 0.1)
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  smith-waterman (writing parameters)
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  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 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
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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 (0.7 sec)
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- water time: 0.8 (ig-sw 0.7 processing 0.1)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (1.5 sec)
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+ water time: 1.8 (ig-sw 1.6 processing 0.2)
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  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
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92
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
93
- (0.4 sec)
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+ (0.7 sec)
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  hmm
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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 (0.6 sec)
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- infra time: 0.7
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- hmm step time: 1.0
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (1.0 sec)
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+ infra time: 1.2
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+ hmm step time: 1.6
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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
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- (0.4 sec)
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- total time: 3.1
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+ (0.6 sec)
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+ total time: 5.3
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
@@ -113,30 +113,30 @@ smith-waterman (new-allele fitting)
113
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  running 10 procs for 11 seqs
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  info for 11 / 11 = 1.000 (removed: 0 failed)
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  kept 7 (0.636) unproductive
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- water time: 0.1 (ig-sw 0.0 processing 0.1)
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+ water time: 0.2 (ig-sw 0.0 processing 0.2)
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  smith-waterman (writing parameters)
118
- 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
120
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  info for 11 / 11 = 1.000 (removed: 0 failed)
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  kept 7 (0.636) unproductive
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
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- 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: 0.6 (ig-sw 0.5 processing 0.2)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.7 sec)
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+ water time: 1.0 (ig-sw 0.8 processing 0.2)
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  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
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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
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- (0.3 sec)
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+ (0.5 sec)
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  hmm
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  reading output
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  read 11 hmm output lines with 11 sequences in 11 events (0 failures)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.3 sec)
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- infra time: 0.4
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- hmm step time: 0.7
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.6 sec)
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+ infra time: 0.7
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+ hmm step time: 1.0
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  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
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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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- (0.2 sec)
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- total time: 2.3
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+ (0.3 sec)
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+ total time: 3.3
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  partition igh:
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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
@@ -148,56 +148,56 @@ smith-waterman
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  kept 14 (0.438) unproductive
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  water time: 0.0
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  hmm
151
- caching all 32 naive sequences (0.6s)
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+ caching all 32 naive sequences (1.1s)
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  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
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- 30 clusters with 10 procs (0.4s)
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- 29 clusters with 7 procs (0.5s)
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- 28 clusters with 5 procs (0.4s)
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- 28 clusters with 3 procs (0.4s)
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- 23 clusters with 2 procs (0.5s)
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- 20 clusters with 1 proc (0.8s)
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+ 30 clusters with 10 procs (0.5s)
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+ 29 clusters with 7 procs (0.6s)
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+ 28 clusters with 5 procs (0.6s)
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+ 28 clusters with 3 procs (0.7s)
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+ 23 clusters with 2 procs (0.7s)
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+ 20 clusters with 1 proc (1.2s)
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  note not merging entire cpath history
160
- partition loop time: 3.0
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+ partition loop time: 4.3
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  getting annotations for final partition
162
- subcluster annotating 16 clusters with steps: (0.5s) (0.2s)
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- subcluster annotation time 0.7
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- total time: 4.5
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+ subcluster annotating 16 clusters with steps: (0.8s) (0.3s)
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+ subcluster annotation time 1.0
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+ total time: 6.7
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
167
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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
168
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  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
169
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  smith-waterman
170
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
172
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  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
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  kept 9 (0.500) unproductive
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  water time: 0.0
175
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  hmm
176
- caching all 18 naive sequences (0.4s)
176
+ caching all 18 naive sequences (0.5s)
177
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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 (0.2s)
181
- 7 clusters with 3 procs (0.2s)
180
+ 7 clusters with 5 procs (0.3s)
181
+ 7 clusters with 3 procs (0.3s)
182
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  6 clusters with 2 procs (0.2s)
183
- 6 clusters with 1 proc (0.3s)
184
- partition loop time: 1.2
183
+ 6 clusters with 1 proc (0.4s)
184
+ partition loop time: 1.4
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185
  getting annotations for final partition
186
- subcluster annotating 6 clusters with steps: (0.3s) (0.1s)
187
- subcluster annotation time 0.4
188
- total time: 2.2
186
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s)
187
+ subcluster annotation time 0.6
188
+ total time: 2.6
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189
  partition igl:
190
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  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)
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  smith-waterman
194
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
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+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
195
195
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
196
196
  info for 11 / 11 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
197
197
  kept 7 (0.636) unproductive
198
198
  water time: 0.0
199
199
  hmm
200
- caching all 11 naive sequences (0.2s)
200
+ caching all 11 naive sequences (0.3s)
201
201
  collapsed 11 queries into 3 clusters with identical naive seqs (0.0 sec)
202
202
  reducing n procs to number of clusters: 10 --> 3
203
203
  3 clusters with 3 procs (0.2s)
@@ -206,7 +206,7 @@ hmm
206
206
  partition loop time: 0.6
207
207
  getting annotations for final partition
208
208
  subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
209
- subcluster annotation time 0.3
209
+ subcluster annotation time 0.4
210
210
  total time: 1.4
211
211
  combining chains
212
212
  cleaning pair info for 61 seqs
@@ -227,6 +227,7 @@ cleaning pair info for 61 seqs
227
227
  k 0 0 1
228
228
  merge time 0.0
229
229
  need to get annotations for 2/11 joint igh clusters
230
+ tag: v1.0.13
230
231
  annotate igh+igk: igh
231
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
232
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
@@ -239,17 +240,18 @@ smith-waterman
239
240
  kept 7 (0.368) unproductive
240
241
  water time: 0.0
241
242
  hmm
242
- subcluster annotating 11 clusters with steps: (0.4s) (0.2s)
243
- subcluster annotation time 0.6
244
- total time: 0.7
243
+ subcluster annotating 11 clusters with steps: (0.6s) (0.2s)
244
+ subcluster annotation time 0.8
245
+ total time: 1.0
245
246
  need to get annotations for 6/11 joint igk clusters
247
+ tag: v1.0.13
246
248
  annotate igh+igk: igk
247
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
248
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
249
251
  --input-partition-fname: read best partition with 18 sequences in 11 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
250
252
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
251
253
  smith-waterman
252
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
254
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
253
255
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
254
256
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
255
257
  kept 9 (0.500) unproductive
@@ -257,8 +259,9 @@ smith-waterman
257
259
  hmm
258
260
  reading output
259
261
  read 11 hmm output lines with 18 sequences in 11 events (0 failures)
260
- hmm step time: 0.3
261
- total time: 0.5
262
+ infra time: 0.1
263
+ hmm step time: 0.4
264
+ total time: 0.6
262
265
  igh+igl: synchronizing heavy and light chain cluster paths
263
266
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
264
267
  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
@@ -275,6 +278,7 @@ hmm
275
278
  l 0 0 1
276
279
  merge time 0.0
277
280
  need to get annotations for 2/5 joint igh clusters
281
+ tag: v1.0.13
278
282
  annotate igh+igl: igh
279
283
  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
280
284
  --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
@@ -287,10 +291,11 @@ smith-waterman
287
291
  kept 7 (0.583) unproductive
288
292
  water time: 0.0
289
293
  hmm
290
- subcluster annotating 5 clusters with steps: (0.3s) (0.3s)
291
- subcluster annotation time 0.6
292
- total time: 0.7
294
+ subcluster annotating 5 clusters with steps: (0.4s) (0.3s)
295
+ subcluster annotation time 0.7
296
+ total time: 0.8
293
297
  need to get annotations for 5/5 joint igl clusters
298
+ tag: v1.0.13
294
299
  annotate igh+igl: igl
295
300
  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
296
301
  --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
@@ -303,7 +308,7 @@ smith-waterman
303
308
  kept 7 (0.636) unproductive
304
309
  water time: 0.0
305
310
  hmm
306
- subcluster annotating 5 clusters with steps: (0.2s) (0.3s)
311
+ subcluster annotating 5 clusters with steps: (0.3s) (0.2s)
307
312
  subcluster annotation time 0.5
308
313
  total time: 0.6
309
314
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
@@ -318,4 +323,4 @@ hmm
318
323
  h 16 --> 16
319
324
  k 6 --> 11 +5
320
325
  l 3 --> 5 +2
321
- total time: 39.9
326
+ total time: 60.9
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -27,16 +27,16 @@ hmm
27
27
  caching input annotation naive seqs in bcrham cache file for 27 clusters (53 seqs)
28
28
  --continue-from-input-partition: using input partition for initial cpath
29
29
  27 clusters (53 seqs)
30
- 27 clusters with 10 procs (0.5s)
31
- 26 clusters with 7 procs (0.5s)
32
- 23 clusters with 5 procs (0.4s)
33
- 22 clusters with 3 procs (0.4s)
34
- 21 clusters with 2 procs (0.3s)
35
- 21 clusters with 1 proc (0.7s)
36
- partition loop time: 2.8
30
+ 27 clusters with 10 procs (0.9s)
31
+ 26 clusters with 7 procs (0.7s)
32
+ 23 clusters with 5 procs (0.9s)
33
+ 22 clusters with 3 procs (0.7s)
34
+ 21 clusters with 2 procs (0.5s)
35
+ 21 clusters with 1 proc (1.2s)
36
+ partition loop time: 5.0
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (0.7s) (0.4s) (0.2s)
39
- subcluster annotation time 1.3
38
+ subcluster annotating 18 clusters with steps: (1.1s) (0.5s) (0.3s)
39
+ subcluster annotation time 2.0
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: 4.3
50
+ total time: 7.4
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']
@@ -73,18 +73,18 @@ hmm
73
73
  caching input annotation naive seqs in bcrham cache file for 19 clusters (36 seqs)
74
74
  --continue-from-input-partition: using input partition for initial cpath
75
75
  19 clusters (36 seqs)
76
- 19 clusters with 10 procs (0.3s)
76
+ 19 clusters with 10 procs (0.4s)
77
77
  17 clusters with 7 procs (0.3s)
78
78
  15 clusters with 5 procs (0.3s)
79
- 12 clusters with 3 procs (0.3s)
80
- 11 clusters with 2 procs (0.2s)
79
+ 12 clusters with 3 procs (0.2s)
80
+ 11 clusters with 2 procs (0.3s)
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: 1.9
84
84
  getting annotations for final partition
85
- subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.2s)
85
+ subcluster annotating 6 clusters with steps: (0.5s) (0.2s) (0.2s)
86
86
  subcluster annotation time 0.8
87
- total time: 2.8
87
+ total time: 2.9
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 0.1 sec
105
+ vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.2 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
@@ -113,23 +113,23 @@ hmm
113
113
  --continue-from-input-partition: using input partition for initial cpath
114
114
  8 clusters (18 seqs)
115
115
  reducing n procs to number of clusters: 10 --> 8
116
- 8 clusters with 8 procs (0.2s)
117
- 8 clusters with 6 procs (0.3s)
116
+ 8 clusters with 8 procs (0.3s)
117
+ 8 clusters with 6 procs (0.4s)
118
118
  7 clusters with 4 procs (0.2s)
119
119
  6 clusters with 3 procs (0.2s)
120
120
  6 clusters with 2 procs (0.2s)
121
- 3 clusters with 1 proc (0.2s)
122
- partition loop time: 1.3
121
+ 3 clusters with 1 proc (0.6s)
122
+ partition loop time: 1.9
123
123
  getting annotations for final partition
124
- subcluster annotating 3 clusters with steps: (0.2s) (0.2s) (0.2s)
125
- subcluster annotation time 0.6
124
+ subcluster annotating 3 clusters with steps: (0.4s) (0.2s) (0.1s)
125
+ subcluster annotation time 0.8
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: 2.0
132
+ total time: 2.9
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
@@ -165,6 +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: v1.0.13
168
169
  annotate igh+igk: igh
169
170
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
170
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
@@ -178,10 +179,11 @@ smith-waterman
178
179
  kept 13 (0.371) unproductive
179
180
  water time: 0.0
180
181
  hmm
181
- subcluster annotating 15 clusters with steps: (0.5s) (0.3s)
182
- subcluster annotation time 0.8
183
- total time: 1.0
182
+ subcluster annotating 15 clusters with steps: (0.8s) (0.2s)
183
+ subcluster annotation time 1.0
184
+ total time: 1.2
184
185
  need to get annotations for 13/15 joint igk clusters
186
+ tag: v1.0.13
185
187
  annotate igh+igk: igk
186
188
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
187
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
@@ -195,9 +197,9 @@ smith-waterman
195
197
  kept 14 (0.389) unproductive
196
198
  water time: 0.0
197
199
  hmm
198
- subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
199
- subcluster annotation time 0.7
200
- total time: 0.9
200
+ subcluster annotating 15 clusters with steps: (0.7s) (0.2s)
201
+ subcluster annotation time 1.0
202
+ total time: 1.1
201
203
  igh+igl: synchronizing heavy and light chain cluster paths
202
204
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
203
205
  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
@@ -226,6 +228,7 @@ hmm
226
228
  joint 1.000 0.787
227
229
  merge time 0.0
228
230
  need to get annotations for 2/6 joint igh clusters
231
+ tag: v1.0.13
229
232
  annotate igh+igl: igh
230
233
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
231
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
@@ -233,16 +236,17 @@ hmm
233
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
234
237
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
235
238
  smith-waterman
236
- 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 0.7 sec
237
240
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
238
241
  info for 19 / 19 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
239
242
  kept 11 (0.579) unproductive
240
- water time: 0.0
243
+ water time: 0.1
241
244
  hmm
242
- subcluster annotating 6 clusters with steps: (0.4s) (0.3s) (0.3s)
243
- subcluster annotation time 1.0
244
- total time: 1.2
245
+ subcluster annotating 6 clusters with steps: (0.7s) (0.3s) (0.3s)
246
+ subcluster annotation time 1.4
247
+ total time: 2.2
245
248
  need to get annotations for 6/6 joint igl clusters
249
+ tag: v1.0.13
246
250
  annotate igh+igl: igl
247
251
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
248
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
@@ -256,9 +260,9 @@ smith-waterman
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  kept 13 (0.722) unproductive
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  water time: 0.0
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  hmm
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- subcluster annotating 6 clusters with steps: (0.3s) (0.2s) (0.1s)
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- subcluster annotation time 0.6
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- total time: 0.7
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+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.2s)
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+ subcluster annotation time 0.8
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+ total time: 1.0
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  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml
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  concatenating heavy chain loci:
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  h starting with 15 annotations (35 seqs)
@@ -272,4 +276,4 @@ hmm
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  h 18 --> 21 +3
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  k 6 --> 15 +9
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  l 3 --> 6 +3
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- total time: 26.5
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+ total time: 43.5