partis-bcr 1.0.12.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13__cp312-cp312-macosx_10_13_universal2.whl

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Files changed (50) hide show
  1. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/RECORD +50 -50
  3. test/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  4. test/new-results/partition-new-simu/fasttree/iclust-2/log +3 -3
  5. test/new-results/run-times.csv +7 -7
  6. test/new-results/test.log +43 -43
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  10. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +3 -3
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +2 -2
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +1 -1
  13. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +1 -1
  14. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +4 -4
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  30. test/paired/new-results/run-times.csv +6 -6
  31. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +66 -62
  32. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +48 -44
  33. test/paired/new-results/subset-partition-new-simu/merged-partition.log +38 -34
  34. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  36. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  37. test/paired/new-results/test.log +140 -131
  38. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/cf-alleles.py +0 -0
  39. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/cf-germlines.py +0 -0
  40. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/compare-plotdirs.py +0 -0
  41. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/extract-pairing-info.py +0 -0
  42. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/gctree-run.py +0 -0
  43. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/get-naive-probabilities.py +0 -0
  44. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/parse-output.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/partis-test.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/split-loci.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/WHEEL +0 -0
  48. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/entry_points.txt +0 -0
  49. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/licenses/COPYING +0 -0
  50. {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -36,37 +36,37 @@ 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
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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
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- 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: 0.2 (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 0.1 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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  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 (1.0 sec)
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- water time: 1.3 (ig-sw 1.2 processing 0.2)
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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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- (1.3 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 (2.5 sec)
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- infra time: 3.1
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- hmm step time: 4.6
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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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- (1.1 sec)
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- total time: 9.0
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+ (0.9 sec)
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+ total time: 6.5
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  cache-parameters igk:
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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
@@ -74,34 +74,34 @@ 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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  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
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- water time: 0.2 (ig-sw 0.0 processing 0.2)
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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
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.8 sec)
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- water time: 1.1 (ig-sw 0.9 processing 0.2)
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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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  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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+ (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 (0.8 sec)
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- infra time: 0.9
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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 (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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  (0.6 sec)
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- total time: 4.1
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+ total time: 5.3
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  cache-parameters igl:
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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
@@ -120,48 +120,48 @@ smith-waterman (writing parameters)
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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 (0.6 sec)
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- water time: 0.8 (ig-sw 0.6 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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  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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+ (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 (0.5 sec)
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- infra time: 0.6
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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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  (0.3 sec)
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- total time: 3.1
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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
142
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  --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
143
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  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
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  smith-waterman
145
- vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
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+ vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
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  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
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  info for 32 / 32 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
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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 (0.9s)
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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 (0.5s)
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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 (0.6s)
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+ 28 clusters with 3 procs (0.7s)
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  23 clusters with 2 procs (0.7s)
158
- 20 clusters with 1 proc (0.9s)
158
+ 20 clusters with 1 proc (1.2s)
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  note not merging entire cpath history
160
- partition loop time: 3.7
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+ partition loop time: 4.3
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  getting annotations for final partition
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  subcluster annotating 16 clusters with steps: (0.8s) (0.3s)
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  subcluster annotation time 1.0
164
- total time: 5.9
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+ total time: 6.7
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  partition igk:
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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
@@ -176,15 +176,15 @@ hmm
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  caching all 18 naive sequences (0.5s)
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  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
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  reducing n procs to number of clusters: 10 --> 7
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- 7 clusters with 7 procs (0.4s)
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+ 7 clusters with 7 procs (0.3s)
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  7 clusters with 5 procs (0.3s)
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  7 clusters with 3 procs (0.3s)
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- 6 clusters with 2 procs (0.1s)
182
+ 6 clusters with 2 procs (0.2s)
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  6 clusters with 1 proc (0.4s)
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  partition loop time: 1.4
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  getting annotations for final partition
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- subcluster annotating 6 clusters with steps: (0.4s) (0.1s)
187
- subcluster annotation time 0.5
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+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s)
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+ subcluster annotation time 0.6
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  total time: 2.6
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  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
@@ -197,17 +197,17 @@ smith-waterman
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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)
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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
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  3 clusters with 3 procs (0.2s)
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  3 clusters with 2 procs (0.2s)
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  3 clusters with 1 proc (0.3s)
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- partition loop time: 0.7
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+ partition loop time: 0.6
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  getting annotations for final partition
208
- subcluster annotating 3 clusters with steps: (0.3s) (0.3s)
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- subcluster annotation time 0.6
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- total time: 1.9
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+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
209
+ subcluster annotation time 0.4
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
@@ -227,6 +227,7 @@ cleaning pair info for 61 seqs
227
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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: v1.0.13
230
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  annotate igh+igk: igh
231
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  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
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  --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
@@ -243,13 +244,14 @@ hmm
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  subcluster annotation time 0.8
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  total time: 1.0
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  need to get annotations for 6/11 joint igk clusters
247
+ tag: v1.0.13
246
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  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
@@ -258,7 +260,7 @@ hmm
258
260
  reading output
259
261
  read 11 hmm output lines with 18 sequences in 11 events (0 failures)
260
262
  infra time: 0.1
261
- hmm step time: 0.5
263
+ hmm step time: 0.4
262
264
  total time: 0.6
263
265
  igh+igl: synchronizing heavy and light chain cluster paths
264
266
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
@@ -276,6 +278,7 @@ hmm
276
278
  l 0 0 1
277
279
  merge time 0.0
278
280
  need to get annotations for 2/5 joint igh clusters
281
+ tag: v1.0.13
279
282
  annotate igh+igl: igh
280
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
281
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
@@ -292,6 +295,7 @@ hmm
292
295
  subcluster annotation time 0.7
293
296
  total time: 0.8
294
297
  need to get annotations for 5/5 joint igl clusters
298
+ tag: v1.0.13
295
299
  annotate igh+igl: igl
296
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
297
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
@@ -319,4 +323,4 @@ hmm
319
323
  h 16 --> 16
320
324
  k 6 --> 11 +5
321
325
  l 3 --> 5 +2
322
- total time: 56.3
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 (0.6s)
31
- 26 clusters with 7 procs (0.6s)
32
- 23 clusters with 5 procs (0.5s)
33
- 22 clusters with 3 procs (0.5s)
34
- 21 clusters with 2 procs (0.4s)
35
- 21 clusters with 1 proc (0.9s)
36
- partition loop time: 3.5
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: (1.0s) (0.5s) (0.3s)
39
- subcluster annotation time 1.8
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: 5.5
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']
@@ -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 (0.2s)
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
83
  partition loop time: 1.9
84
84
  getting annotations for final partition
85
85
  subcluster annotating 6 clusters with steps: (0.5s) (0.2s) (0.2s)
86
- subcluster annotation time 1.0
87
- total time: 3.1
86
+ subcluster annotation time 0.8
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
@@ -114,22 +114,22 @@ hmm
114
114
  8 clusters (18 seqs)
115
115
  reducing n procs to number of clusters: 10 --> 8
116
116
  8 clusters with 8 procs (0.3s)
117
- 8 clusters with 6 procs (0.3s)
118
- 7 clusters with 4 procs (0.3s)
117
+ 8 clusters with 6 procs (0.4s)
118
+ 7 clusters with 4 procs (0.2s)
119
119
  6 clusters with 3 procs (0.2s)
120
120
  6 clusters with 2 procs (0.2s)
121
- 3 clusters with 1 proc (0.3s)
122
- partition loop time: 1.5
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: (0.3s) (0.2s) (0.3s)
125
- subcluster annotation time 0.7
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: 2.4
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
@@ -172,16 +173,17 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
172
173
  --input-partition-fname: read best partition with 35 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml
173
174
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
174
175
  smith-waterman
175
- vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.2 sec
176
+ vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.1 sec
176
177
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
177
178
  info for 35 / 35 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
178
179
  kept 13 (0.371) unproductive
179
180
  water time: 0.0
180
181
  hmm
181
- subcluster annotating 15 clusters with steps: (0.7s) (0.3s)
182
+ subcluster annotating 15 clusters with steps: (0.8s) (0.2s)
182
183
  subcluster annotation time 1.0
183
- total time: 1.3
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: (0.6s) (0.2s)
199
- subcluster annotation time 0.9
200
- total time: 1.0
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: (0.6s) (0.3s) (0.4s)
243
- subcluster annotation time 1.3
244
- total time: 1.4
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
@@ -258,7 +262,7 @@ smith-waterman
258
262
  hmm
259
263
  subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.2s)
260
264
  subcluster annotation time 0.8
261
- total time: 0.9
265
+ total time: 1.0
262
266
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml
263
267
  concatenating heavy chain loci:
264
268
  h starting with 15 annotations (35 seqs)
@@ -272,4 +276,4 @@ hmm
272
276
  h 18 --> 21 +3
273
277
  k 6 --> 15 +9
274
278
  l 3 --> 6 +3
275
- total time: 33.0
279
+ total time: 43.5