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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (51) hide show
  1. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/METADATA +1 -1
  2. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/RECORD +51 -51
  3. python/processargs.py +4 -1
  4. test/new-results/partition-new-simu/fasttree/iclust-0/log +5 -5
  5. test/new-results/partition-new-simu/fasttree/iclust-1/log +3 -3
  6. test/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  7. test/new-results/run-times.csv +8 -8
  8. test/new-results/test.log +52 -52
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +2 -2
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +2 -2
  12. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +6 -6
  13. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +1 -1
  14. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +3 -3
  15. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +4 -4
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +108 -108
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +84 -84
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +62 -62
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +19 -19
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +25 -25
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +36 -36
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +23 -23
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +46 -46
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +46 -46
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +46 -46
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +16 -16
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +16 -16
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +48 -48
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +49 -49
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +28 -28
  31. test/paired/new-results/run-times.csv +6 -6
  32. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +51 -55
  33. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +51 -55
  34. test/paired/new-results/subset-partition-new-simu/merged-partition.log +37 -41
  35. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  36. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  37. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  38. test/paired/new-results/test.log +146 -155
  39. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/cf-alleles.py +0 -0
  40. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/cf-germlines.py +0 -0
  41. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/compare-plotdirs.py +0 -0
  42. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/extract-pairing-info.py +0 -0
  43. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/gctree-run.py +0 -0
  44. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/get-naive-probabilities.py +0 -0
  45. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/parse-output.py +0 -0
  46. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/partis-test.py +0 -0
  47. {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev4.data}/scripts/split-loci.py +0 -0
  48. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/WHEEL +0 -0
  49. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/entry_points.txt +0 -0
  50. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/licenses/COPYING +0 -0
  51. {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev4.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -39,34 +39,34 @@ caching parameters
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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 0.2 sec
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+ vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
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  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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+ water time: 0.2 (ig-sw 0.0 processing 0.1)
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  smith-waterman (writing parameters)
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- vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
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+ 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 (1.3 sec)
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- water time: 1.6 (ig-sw 1.5 processing 0.2)
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+ water time: 1.6 (ig-sw 1.5 processing 0.1)
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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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- (1.0 sec)
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+ (0.9 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 (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 parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.9 sec)
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+ infra time: 1.0
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+ hmm step time: 1.7
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  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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  (0.9 sec)
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- total time: 6.5
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+ total time: 5.9
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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 0.2 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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  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 0.1)
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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: 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 (1.5 sec)
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- water time: 1.8 (ig-sw 1.6 processing 0.2)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.7 sec)
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+ water time: 1.0 (ig-sw 0.8 processing 0.2)
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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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- (0.7 sec)
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+ (0.5 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 (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 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: 1.2
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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: 5.3
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+ (0.5 sec)
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+ total time: 3.7
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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
@@ -120,12 +120,12 @@ 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 (0.7 sec)
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- water time: 1.0 (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/igl/sw (1.0 sec)
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+ water time: 1.2 (ig-sw 1.1 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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- (0.5 sec)
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+ (0.6 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)
@@ -136,7 +136,7 @@ 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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  (0.3 sec)
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- total time: 3.3
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+ total time: 3.8
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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
@@ -151,63 +151,63 @@ hmm
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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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+ 29 clusters with 7 procs (0.5s)
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  28 clusters with 5 procs (0.6s)
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  28 clusters with 3 procs (0.7s)
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- 23 clusters with 2 procs (0.7s)
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- 20 clusters with 1 proc (1.2s)
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+ 23 clusters with 2 procs (0.8s)
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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: 4.3
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+ partition loop time: 3.9
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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
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- total time: 6.7
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+ subcluster annotating 16 clusters with steps: (0.8s) (0.2s)
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+ subcluster annotation time 1.1
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+ total time: 6.3
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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
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  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
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  smith-waterman
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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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  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
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  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
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  kept 9 (0.500) unproductive
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  water time: 0.0
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  hmm
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- caching all 18 naive sequences (0.5s)
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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 (0.3s)
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- 6 clusters with 2 procs (0.2s)
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+ 7 clusters with 3 procs (0.2s)
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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: 1.4
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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: (0.4s) (0.2s)
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+ subcluster annotating 6 clusters with steps: (0.4s) (0.1s)
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  subcluster annotation time 0.6
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- total time: 2.6
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+ total time: 2.5
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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
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  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
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  smith-waterman
194
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
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+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
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  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
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  info for 11 / 11 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
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  kept 7 (0.636) unproductive
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  water time: 0.0
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  hmm
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- caching all 11 naive sequences (0.3s)
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+ caching all 11 naive sequences (0.4s)
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  collapsed 11 queries into 3 clusters with identical naive seqs (0.0 sec)
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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: 0.6
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+ 3 clusters with 1 proc (0.4s)
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+ partition loop time: 0.8
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  getting annotations for final partition
208
- subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
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+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
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  subcluster annotation time 0.4
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- total time: 1.4
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+ total time: 1.7
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  combining chains
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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
@@ -227,7 +227,6 @@ 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: v1.0.13
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  annotate igh+igk: igh
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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
@@ -242,16 +241,15 @@ smith-waterman
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  hmm
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  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: 1.0
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+ total time: 0.9
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  need to get annotations for 6/11 joint igk clusters
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- tag: v1.0.13
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  annotate igh+igk: igk
249
247
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
250
248
  --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
251
249
  --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
252
250
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
253
251
  smith-waterman
254
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
252
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
255
253
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
256
254
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
257
255
  kept 9 (0.500) unproductive
@@ -260,7 +258,7 @@ hmm
260
258
  reading output
261
259
  read 11 hmm output lines with 18 sequences in 11 events (0 failures)
262
260
  infra time: 0.1
263
- hmm step time: 0.4
261
+ hmm step time: 0.5
264
262
  total time: 0.6
265
263
  igh+igl: synchronizing heavy and light chain cluster paths
266
264
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
@@ -278,7 +276,6 @@ hmm
278
276
  l 0 0 1
279
277
  merge time 0.0
280
278
  need to get annotations for 2/5 joint igh clusters
281
- tag: v1.0.13
282
279
  annotate igh+igl: igh
283
280
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
284
281
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -293,9 +290,8 @@ smith-waterman
293
290
  hmm
294
291
  subcluster annotating 5 clusters with steps: (0.4s) (0.3s)
295
292
  subcluster annotation time 0.7
296
- total time: 0.8
293
+ total time: 0.9
297
294
  need to get annotations for 5/5 joint igl clusters
298
- tag: v1.0.13
299
295
  annotate igh+igl: igl
300
296
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
301
297
  --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
@@ -308,9 +304,9 @@ smith-waterman
308
304
  kept 7 (0.636) unproductive
309
305
  water time: 0.0
310
306
  hmm
311
- subcluster annotating 5 clusters with steps: (0.3s) (0.2s)
312
- subcluster annotation time 0.5
313
- total time: 0.6
307
+ subcluster annotating 5 clusters with steps: (0.4s) (0.3s)
308
+ subcluster annotation time 0.6
309
+ total time: 0.7
314
310
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
315
311
  concatenating heavy chain loci:
316
312
  h starting with 11 annotations (19 seqs)
@@ -323,4 +319,4 @@ hmm
323
319
  h 16 --> 16
324
320
  k 6 --> 11 +5
325
321
  l 3 --> 5 +2
326
- total time: 60.9
322
+ total time: 62.1
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 (0.9s)
30
+ 27 clusters with 10 procs (0.7s)
31
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
32
+ 23 clusters with 5 procs (0.6s)
33
+ 22 clusters with 3 procs (0.6s)
34
+ 21 clusters with 2 procs (0.4s)
35
+ 21 clusters with 1 proc (1.1s)
36
+ partition loop time: 4.0
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (1.1s) (0.5s) (0.3s)
39
- subcluster annotation time 2.0
38
+ subcluster annotating 18 clusters with steps: (1.0s) (0.4s) (0.2s)
39
+ subcluster annotation time 1.7
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: 7.4
50
+ total time: 6.0
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
@@ -77,14 +77,14 @@ hmm
77
77
  17 clusters with 7 procs (0.3s)
78
78
  15 clusters with 5 procs (0.3s)
79
79
  12 clusters with 3 procs (0.2s)
80
- 11 clusters with 2 procs (0.3s)
81
- 7 clusters with 1 proc (0.4s)
80
+ 11 clusters with 2 procs (0.2s)
81
+ 7 clusters with 1 proc (0.5s)
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 0.8
87
- total time: 2.9
86
+ subcluster annotation time 0.9
87
+ total time: 3.1
88
88
  partition igl:
89
89
  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igl.yaml --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
90
90
  warning replacing 'paired-uids'/'paired-uids' value for '7588f09c07-igl' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['7588f09c07-igh', 'cb8a759f1a-igh'] --> ['7588f09c07-igh']
@@ -102,7 +102,7 @@ getting annotations for final partition
102
102
  removed 3/21 queries from input info that were absent from input partition
103
103
  partitioning (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm)
104
104
  smith-waterman
105
- vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.2 sec
105
+ vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.1 sec
106
106
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
107
107
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
108
108
  kept 13 (0.722) unproductive
@@ -113,23 +113,23 @@ hmm
113
113
  --continue-from-input-partition: using input partition for initial cpath
114
114
  8 clusters (18 seqs)
115
115
  reducing n procs to number of clusters: 10 --> 8
116
- 8 clusters with 8 procs (0.3s)
117
- 8 clusters with 6 procs (0.4s)
118
- 7 clusters with 4 procs (0.2s)
116
+ 8 clusters with 8 procs (0.2s)
117
+ 8 clusters with 6 procs (0.3s)
118
+ 7 clusters with 4 procs (0.3s)
119
119
  6 clusters with 3 procs (0.2s)
120
120
  6 clusters with 2 procs (0.2s)
121
- 3 clusters with 1 proc (0.6s)
122
- partition loop time: 1.9
121
+ 3 clusters with 1 proc (0.2s)
122
+ partition loop time: 1.4
123
123
  getting annotations for final partition
124
- subcluster annotating 3 clusters with steps: (0.4s) (0.2s) (0.1s)
125
- subcluster annotation time 0.8
124
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s) (0.1s)
125
+ subcluster annotation time 0.6
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: 2.9
132
+ total time: 2.1
133
133
  combining chains
134
134
  cleaning pair info for 107 seqs
135
135
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -165,7 +165,6 @@ 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
169
168
  annotate igh+igk: igh
170
169
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
171
170
  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
@@ -173,17 +172,16 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
173
172
  --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
174
173
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
175
174
  smith-waterman
176
- vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.1 sec
175
+ vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.2 sec
177
176
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
178
177
  info for 35 / 35 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
179
178
  kept 13 (0.371) unproductive
180
179
  water time: 0.0
181
180
  hmm
182
- subcluster annotating 15 clusters with steps: (0.8s) (0.2s)
183
- subcluster annotation time 1.0
181
+ subcluster annotating 15 clusters with steps: (0.7s) (0.3s)
182
+ subcluster annotation time 0.9
184
183
  total time: 1.2
185
184
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.13
187
185
  annotate igh+igk: igk
188
186
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
189
187
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -191,14 +189,14 @@ hmm
191
189
  --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml
192
190
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm)
193
191
  smith-waterman
194
- vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
192
+ vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
195
193
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
196
194
  info for 36 / 36 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
197
195
  kept 14 (0.389) unproductive
198
196
  water time: 0.0
199
197
  hmm
200
- subcluster annotating 15 clusters with steps: (0.7s) (0.2s)
201
- subcluster annotation time 1.0
198
+ subcluster annotating 15 clusters with steps: (0.6s) (0.2s)
199
+ subcluster annotation time 0.8
202
200
  total time: 1.1
203
201
  igh+igl: synchronizing heavy and light chain cluster paths
204
202
  removing badly + unpaired seqs: kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2 l 1
@@ -228,7 +226,6 @@ hmm
228
226
  joint 1.000 0.787
229
227
  merge time 0.0
230
228
  need to get annotations for 2/6 joint igh clusters
231
- tag: v1.0.13
232
229
  annotate igh+igl: igh
233
230
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
234
231
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -236,17 +233,16 @@ hmm
236
233
  --input-partition-fname: read best partition with 19 sequences in 6 clusters from test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml
237
234
  annotating (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
238
235
  smith-waterman
239
- vsearch: 19 / 19 v annotations (0 failed) with 4 v genes in 0.7 sec
236
+ vsearch: 19 / 19 v annotations (0 failed) with 4 v genes in 0.1 sec
240
237
  reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
241
238
  info for 19 / 19 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
242
239
  kept 11 (0.579) unproductive
243
- water time: 0.1
240
+ water time: 0.0
244
241
  hmm
245
- subcluster annotating 6 clusters with steps: (0.7s) (0.3s) (0.3s)
242
+ subcluster annotating 6 clusters with steps: (0.6s) (0.3s) (0.5s)
246
243
  subcluster annotation time 1.4
247
- total time: 2.2
244
+ total time: 1.6
248
245
  need to get annotations for 6/6 joint igl clusters
249
- tag: v1.0.13
250
246
  annotate igh+igl: igl
251
247
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
252
248
  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
@@ -260,9 +256,9 @@ smith-waterman
260
256
  kept 13 (0.722) unproductive
261
257
  water time: 0.0
262
258
  hmm
263
- subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.2s)
264
- subcluster annotation time 0.8
265
- total time: 1.0
259
+ subcluster annotating 6 clusters with steps: (0.4s) (0.2s) (0.1s)
260
+ subcluster annotation time 0.7
261
+ total time: 0.8
266
262
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml
267
263
  concatenating heavy chain loci:
268
264
  h starting with 15 annotations (35 seqs)
@@ -276,4 +272,4 @@ hmm
276
272
  h 18 --> 21 +3
277
273
  k 6 --> 15 +9
278
274
  l 3 --> 6 +3
279
- total time: 43.5
275
+ total time: 34.7