partis-bcr 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12__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 (49) hide show
  1. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/RECORD +49 -49
  3. test/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  4. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  5. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  6. test/new-results/run-times.csv +8 -8
  7. test/new-results/test.log +46 -46
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +6 -6
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +5 -5
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  11. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  12. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +1 -1
  13. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +2 -2
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  29. test/paired/new-results/run-times.csv +6 -6
  30. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +47 -43
  31. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +56 -52
  32. test/paired/new-results/subset-partition-new-simu/merged-partition.log +28 -24
  33. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  34. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  36. test/paired/new-results/test.log +127 -118
  37. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/cf-alleles.py +0 -0
  38. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/cf-germlines.py +0 -0
  39. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/compare-plotdirs.py +0 -0
  40. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/extract-pairing-info.py +0 -0
  41. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/gctree-run.py +0 -0
  42. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/get-naive-probabilities.py +0 -0
  43. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/parse-output.py +0 -0
  44. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/partis-test.py +0 -0
  45. {partis_bcr-1.0.11.post1.dev7.data → partis_bcr-1.0.12.data}/scripts/split-loci.py +0 -0
  46. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/WHEEL +0 -0
  47. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/entry_points.txt +0 -0
  48. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/licenses/COPYING +0 -0
  49. {partis_bcr-1.0.11.post1.dev7.dist-info → partis_bcr-1.0.12.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -43,35 +43,35 @@ smith-waterman (new-allele fitting)
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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 0.1)
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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 0.1 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: 1.1 (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/igh/sw (0.9 sec)
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+ water time: 1.2 (ig-sw 1.0 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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+ (0.8 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: 1.5
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.8 sec)
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+ infra time: 0.9
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+ hmm step time: 1.6
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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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+ (0.7 sec)
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+ total time: 4.8
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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
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  caching parameters
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- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 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
@@ -85,8 +85,8 @@ smith-waterman (writing parameters)
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  info for 18 / 18 = 1.000 (removed: 0 failed)
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  kept 9 (0.500) unproductive
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.7 sec)
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- water time: 0.9 (ig-sw 0.8 processing 0.2)
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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 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
@@ -101,15 +101,15 @@ hmm
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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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  (0.5 sec)
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- total time: 3.7
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+ total time: 3.8
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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
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  caching parameters
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- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
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+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
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  keeping 3 / 80 v genes
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  smith-waterman (new-allele fitting)
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- 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
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  info for 11 / 11 = 1.000 (removed: 0 failed)
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  kept 7 (0.636) unproductive
@@ -120,8 +120,8 @@ 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 (0.4 sec)
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- water time: 0.7 (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 (0.5 sec)
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+ water time: 0.8 (ig-sw 0.6 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
@@ -129,39 +129,39 @@ smith-waterman (writing parameters)
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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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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.4 sec)
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+ infra time: 0.5
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  hmm step time: 0.7
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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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+ total time: 2.5
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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
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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 0.1 sec
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+ vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
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  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
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- caching all 32 naive sequences (0.6s)
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+ caching all 32 naive sequences (0.7s)
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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 5 procs (0.5s)
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  28 clusters with 3 procs (0.5s)
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- 23 clusters with 2 procs (0.6s)
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- 20 clusters with 1 proc (0.7s)
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+ 23 clusters with 2 procs (0.5s)
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+ 20 clusters with 1 proc (0.9s)
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  note not merging entire cpath history
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- partition loop time: 3.1
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+ partition loop time: 3.2
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  getting annotations for final partition
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  subcluster annotating 16 clusters with steps: (0.5s) (0.2s)
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- subcluster annotation time 0.8
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- total time: 4.7
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+ subcluster annotation time 0.7
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+ total time: 4.9
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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
@@ -173,19 +173,19 @@ smith-waterman
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  kept 9 (0.500) unproductive
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  water time: 0.0
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  hmm
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- caching all 18 naive sequences (0.3s)
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+ caching all 18 naive sequences (0.4s)
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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 (0.3s)
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  7 clusters with 5 procs (0.3s)
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  7 clusters with 3 procs (0.2s)
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- 6 clusters with 2 procs (0.2s)
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- 6 clusters with 1 proc (0.3s)
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- partition loop time: 1.2
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+ 6 clusters with 2 procs (0.1s)
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+ 6 clusters with 1 proc (0.4s)
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+ partition loop time: 1.3
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  getting annotations for final partition
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- subcluster annotating 6 clusters with steps: (0.2s) (0.2s)
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- subcluster annotation time 0.4
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- total time: 2.1
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+ subcluster annotating 6 clusters with steps: (0.3s) (0.1s)
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+ subcluster annotation time 0.5
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+ total time: 2.4
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  partition igl:
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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
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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
@@ -202,11 +202,11 @@ hmm
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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 (0.2s)
205
+ 3 clusters with 1 proc (0.3s)
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  partition loop time: 0.6
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  getting annotations for final partition
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- subcluster annotating 3 clusters with steps: (0.3s) (0.2s)
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- subcluster annotation time 0.4
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+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
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+ subcluster annotation time 0.3
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  total time: 1.4
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  combining chains
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  cleaning pair info for 61 seqs
@@ -227,22 +227,24 @@ cleaning pair info for 61 seqs
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  k 0 0 1
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  merge time 0.0
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  need to get annotations for 2/11 joint igh clusters
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+ tag: v1.0.12
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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
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  --input-partition-fname: read best partition with 19 sequences in 11 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
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  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
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  smith-waterman
236
- vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.2 sec
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+ vsearch: 19 / 19 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/igh/sw-cache.yaml
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  info for 19 / 19 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
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  kept 7 (0.368) unproductive
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  water time: 0.0
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  hmm
242
- subcluster annotating 11 clusters with steps: (0.5s) (0.3s)
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- subcluster annotation time 0.7
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- total time: 0.9
243
+ subcluster annotating 11 clusters with steps: (0.6s) (0.2s)
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+ subcluster annotation time 0.8
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+ total time: 0.8
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  need to get annotations for 6/11 joint igk clusters
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+ tag: v1.0.12
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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
@@ -257,8 +259,8 @@ 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: 0.4
262
+ hmm step time: 0.4
263
+ total time: 0.5
262
264
  igh+igl: synchronizing heavy and light chain cluster paths
263
265
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
264
266
  note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -275,6 +277,7 @@ hmm
275
277
  l 0 0 1
276
278
  merge time 0.0
277
279
  need to get annotations for 2/5 joint igh clusters
280
+ tag: v1.0.12
278
281
  annotate igh+igl: igh
279
282
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
280
283
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -287,25 +290,26 @@ smith-waterman
287
290
  kept 7 (0.583) unproductive
288
291
  water time: 0.0
289
292
  hmm
290
- subcluster annotating 5 clusters with steps: (0.3s) (0.2s)
291
- subcluster annotation time 0.6
292
- total time: 0.7
293
+ subcluster annotating 5 clusters with steps: (0.4s) (0.3s)
294
+ subcluster annotation time 0.7
295
+ total time: 0.8
293
296
  need to get annotations for 5/5 joint igl clusters
297
+ tag: v1.0.12
294
298
  annotate igh+igl: igl
295
299
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
296
300
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
297
301
  --input-partition-fname: read best partition with 11 sequences in 5 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
298
302
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
299
303
  smith-waterman
300
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
304
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
301
305
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
302
306
  info for 11 / 11 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
303
307
  kept 7 (0.636) unproductive
304
308
  water time: 0.0
305
309
  hmm
306
- subcluster annotating 5 clusters with steps: (0.3s) (0.1s)
307
- subcluster annotation time 0.4
308
- total time: 0.5
310
+ subcluster annotating 5 clusters with steps: (0.2s) (0.3s)
311
+ subcluster annotation time 0.5
312
+ total time: 0.6
309
313
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
310
314
  concatenating heavy chain loci:
311
315
  h starting with 11 annotations (19 seqs)
@@ -318,4 +322,4 @@ hmm
318
322
  h 16 --> 16
319
323
  k 6 --> 11 +5
320
324
  l 3 --> 5 +2
321
- total time: 43.7
325
+ total time: 47.7
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -28,15 +28,15 @@ hmm
28
28
  --continue-from-input-partition: using input partition for initial cpath
29
29
  27 clusters (53 seqs)
30
30
  27 clusters with 10 procs (0.6s)
31
- 26 clusters with 7 procs (0.5s)
32
- 23 clusters with 5 procs (0.4s)
31
+ 26 clusters with 7 procs (0.6s)
32
+ 23 clusters with 5 procs (0.5s)
33
33
  22 clusters with 3 procs (0.5s)
34
- 21 clusters with 2 procs (0.3s)
34
+ 21 clusters with 2 procs (0.4s)
35
35
  21 clusters with 1 proc (0.7s)
36
36
  partition loop time: 3.1
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (0.7s) (0.4s) (0.3s)
39
- subcluster annotation time 1.5
38
+ subcluster annotating 18 clusters with steps: (0.8s) (0.4s) (0.3s)
39
+ subcluster annotation time 1.6
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: 4.7
50
+ total time: 4.9
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']
@@ -63,7 +63,7 @@ getting annotations for final partition
63
63
  --input-partition-fname: read best partition with 36 sequences in 19 clusters from test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igk.yaml
64
64
  partitioning (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm)
65
65
  smith-waterman
66
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
66
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
67
67
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
68
68
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
69
69
  kept 14 (0.389) unproductive
@@ -73,8 +73,8 @@ 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 (0.4s)
77
- 17 clusters with 7 procs (0.2s)
76
+ 19 clusters with 10 procs (0.3s)
77
+ 17 clusters with 7 procs (0.4s)
78
78
  15 clusters with 5 procs (0.3s)
79
79
  12 clusters with 3 procs (0.2s)
80
80
  11 clusters with 2 procs (0.3s)
@@ -84,7 +84,7 @@ hmm
84
84
  getting annotations for final partition
85
85
  subcluster annotating 6 clusters with steps: (0.4s) (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']
@@ -117,19 +117,19 @@ hmm
117
117
  8 clusters with 6 procs (0.2s)
118
118
  7 clusters with 4 procs (0.2s)
119
119
  6 clusters with 3 procs (0.2s)
120
- 6 clusters with 2 procs (0.2s)
120
+ 6 clusters with 2 procs (0.3s)
121
121
  3 clusters with 1 proc (0.3s)
122
122
  partition loop time: 1.5
123
123
  getting annotations for final partition
124
- subcluster annotating 3 clusters with steps: (0.3s) (0.1s) (0.2s)
125
- subcluster annotation time 0.6
124
+ subcluster annotating 3 clusters with steps: (0.3s) (0.2s) (0.2s)
125
+ subcluster annotation time 0.7
126
126
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
127
127
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
128
128
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
129
129
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
130
130
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
131
131
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
132
- total time: 2.2
132
+ total time: 2.4
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: v1.0.12
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
@@ -179,9 +180,10 @@ smith-waterman
179
180
  water time: 0.0
180
181
  hmm
181
182
  subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
182
- subcluster annotation time 0.7
183
- total time: 0.9
183
+ subcluster annotation time 0.8
184
+ total time: 1.0
184
185
  need to get annotations for 13/15 joint igk clusters
186
+ tag: v1.0.12
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) (0.1s)
199
- subcluster annotation time 0.6
200
- total time: 0.8
200
+ subcluster annotating 15 clusters with steps: (0.6s) (0.2s)
201
+ subcluster annotation time 0.7
202
+ total time: 0.9
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: v1.0.12
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
@@ -239,10 +242,11 @@ smith-waterman
239
242
  kept 11 (0.579) unproductive
240
243
  water time: 0.0
241
244
  hmm
242
- subcluster annotating 6 clusters with steps: (0.4s) (0.4s) (0.3s)
243
- subcluster annotation time 1.1
245
+ subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.3s)
246
+ subcluster annotation time 1.0
244
247
  total time: 1.2
245
248
  need to get annotations for 6/6 joint igl clusters
249
+ tag: v1.0.12
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
@@ -250,7 +254,7 @@ hmm
250
254
  --input-partition-fname: read best partition with 18 sequences in 6 clusters from test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml
251
255
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm)
252
256
  smith-waterman
253
- vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.1 sec
257
+ vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.2 sec
254
258
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
255
259
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
256
260
  kept 13 (0.722) unproductive
@@ -258,7 +262,7 @@ smith-waterman
258
262
  hmm
259
263
  subcluster annotating 6 clusters with steps: (0.3s) (0.2s) (0.2s)
260
264
  subcluster annotation time 0.7
261
- total time: 0.8
265
+ total time: 0.9
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: 27.4
279
+ total time: 30.4