partis-bcr 1.0.10__cp312-cp312-macosx_10_13_universal2.whl → 1.0.10.post1.dev1__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 (46) hide show
  1. bin/parse-output.py +2 -2
  2. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/parse-output.py +2 -2
  3. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/RECORD +46 -46
  5. test/new-results/test.log +8 -8
  6. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +4 -4
  7. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +4 -4
  9. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +1 -1
  10. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
  11. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  12. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  13. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  14. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  15. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  16. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  17. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  18. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  19. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  20. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  26. test/paired/new-results/run-times.csv +6 -6
  27. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +51 -55
  28. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +48 -53
  29. test/paired/new-results/subset-partition-new-simu/merged-partition.log +24 -28
  30. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  31. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  32. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  33. test/paired/new-results/test.log +130 -139
  34. test/phylo-naive-run.py +1 -1
  35. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  36. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  37. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  38. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  39. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/gctree-run.py +0 -0
  40. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  41. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/partis-test.py +0 -0
  42. {partis_bcr-1.0.10.data → partis_bcr-1.0.10.post1.dev1.data}/scripts/split-loci.py +0 -0
  43. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/WHEEL +0 -0
  44. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/entry_points.txt +0 -0
  45. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.dist-info}/licenses/COPYING +0 -0
  46. {partis_bcr-1.0.10.dist-info → partis_bcr-1.0.10.post1.dev1.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 0.1 sec
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  keeping 6 / 198 v genes
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  smith-waterman (new-allele fitting)
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- vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
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+ vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.3 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 0.1 processing 0.1)
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+ water time: 0.2 (ig-sw 0.0 processing 0.2)
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  smith-waterman (writing parameters)
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  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
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  running 10 procs for 32 seqs
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  info for 32 / 32 = 1.000 (removed: 0 failed)
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  kept 14 (0.438) unproductive
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (2.2 sec)
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- water time: 2.5 (ig-sw 2.3 processing 0.2)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (1.0 sec)
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+ water time: 1.3 (ig-sw 1.1 processing 0.2)
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  writing hmms removed 18 genes from glfo (leaving v 6 d 16 j 4)
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  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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+ (0.8 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 (1.1 sec)
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- infra time: 1.2
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- hmm step time: 2.0
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.9 sec)
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+ infra time: 1.1
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+ hmm step time: 1.7
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  writing hmms removed 3 genes from glfo (leaving v 6 d 13 j 4)
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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- (0.8 sec)
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- total time: 7.1
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+ (0.7 sec)
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+ total time: 5.4
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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
@@ -74,7 +74,7 @@ caching parameters
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  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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  keeping 5 / 64 v genes
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  smith-waterman (new-allele fitting)
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- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
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+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
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  running 10 procs for 18 seqs
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  info for 18 / 18 = 1.000 (removed: 0 failed)
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  kept 9 (0.500) unproductive
@@ -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 (1.0 sec)
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- water time: 1.3 (ig-sw 1.1 processing 0.1)
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.8 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
@@ -94,34 +94,34 @@ smith-waterman (writing parameters)
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  hmm
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  reading output
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  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.8 sec)
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- infra time: 1.0
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- hmm step time: 1.3
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+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.7 sec)
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+ infra time: 0.8
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+ hmm step time: 1.1
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  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
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  (0.5 sec)
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- total time: 4.2
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+ total time: 3.8
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  cache-parameters igl:
106
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  run partis cache-parameters --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
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  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
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  caching parameters
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- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
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+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 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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  running 10 procs for 11 seqs
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  info for 11 / 11 = 1.000 (removed: 0 failed)
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  kept 7 (0.636) unproductive
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- water time: 0.2 (ig-sw 0.0 processing 0.2)
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+ water time: 0.1 (ig-sw 0.0 processing 0.1)
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  smith-waterman (writing parameters)
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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 0.0 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
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  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
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- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.6 sec)
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- water time: 0.8 (ig-sw 0.7 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: 0.7 (ig-sw 0.6 processing 0.1)
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  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
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127
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  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -129,14 +129,14 @@ 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)
132
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.5 sec)
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- infra time: 0.6
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- hmm step time: 0.9
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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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  (0.3 sec)
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- total time: 2.9
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+ total time: 2.6
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  partition igh:
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  run partis partition --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
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  --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -148,50 +148,50 @@ smith-waterman
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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 (0.9s)
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+ caching all 32 naive sequences (0.8s)
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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 (0.4s)
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- 28 clusters with 5 procs (0.5s)
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+ 30 clusters with 10 procs (0.4s)
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+ 29 clusters with 7 procs (0.5s)
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+ 28 clusters with 5 procs (0.4s)
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  28 clusters with 3 procs (0.5s)
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- 23 clusters with 2 procs (0.7s)
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+ 23 clusters with 2 procs (0.6s)
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  20 clusters with 1 proc (0.8s)
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  note not merging entire cpath history
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- partition loop time: 3.5
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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: (0.6s) (0.3s)
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  subcluster annotation time 0.9
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- total time: 5.6
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+ total time: 5.1
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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 (0.4s)
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+ caching all 18 naive sequences (0.3s)
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  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
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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 (0.1s)
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+ 6 clusters with 2 procs (0.2s)
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  6 clusters with 1 proc (0.4s)
184
- partition loop time: 1.4
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+ partition loop time: 1.5
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  getting annotations for final partition
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- subcluster annotating 6 clusters with steps: (0.4s) (0.1s)
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+ subcluster annotating 6 clusters with steps: (0.3s) (0.1s)
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  subcluster annotation time 0.5
188
- total time: 2.4
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+ total time: 2.5
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  partition igl:
190
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  run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
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  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
192
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  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
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  smith-waterman
194
- vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
194
+ vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 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
@@ -201,13 +201,13 @@ hmm
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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)
204
- 3 clusters with 2 procs (0.3s)
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+ 3 clusters with 2 procs (0.2s)
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  3 clusters with 1 proc (0.3s)
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  partition loop time: 0.7
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  getting annotations for final partition
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  subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
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- subcluster annotation time 0.4
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- total time: 1.6
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+ subcluster annotation time 0.3
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+ total time: 1.5
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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: v1.0.10
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  annotate igh+igk: igh
232
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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
@@ -240,11 +239,10 @@ smith-waterman
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  kept 7 (0.368) unproductive
241
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  water time: 0.0
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  hmm
243
- subcluster annotating 11 clusters with steps: (0.5s) (0.3s)
244
- subcluster annotation time 0.7
245
- total time: 0.9
242
+ subcluster annotating 11 clusters with steps: (0.5s) (0.2s)
243
+ subcluster annotation time 0.6
244
+ total time: 0.8
246
245
  need to get annotations for 6/11 joint igk clusters
247
- tag: v1.0.10
248
246
  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
@@ -259,7 +257,6 @@ smith-waterman
259
257
  hmm
260
258
  reading output
261
259
  read 11 hmm output lines with 18 sequences in 11 events (0 failures)
262
- infra time: 0.1
263
260
  hmm step time: 0.4
264
261
  total time: 0.5
265
262
  igh+igl: synchronizing heavy and light chain cluster paths
@@ -278,7 +275,6 @@ hmm
278
275
  l 0 0 1
279
276
  merge time 0.0
280
277
  need to get annotations for 2/5 joint igh clusters
281
- tag: v1.0.10
282
278
  annotate igh+igl: igh
283
279
  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
280
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -292,10 +288,9 @@ smith-waterman
292
288
  water time: 0.0
293
289
  hmm
294
290
  subcluster annotating 5 clusters with steps: (0.3s) (0.3s)
295
- subcluster annotation time 0.6
291
+ subcluster annotation time 0.7
296
292
  total time: 0.8
297
293
  need to get annotations for 5/5 joint igl clusters
298
- tag: v1.0.10
299
294
  annotate igh+igl: igl
300
295
  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
296
  --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
@@ -323,4 +318,4 @@ hmm
323
318
  h 16 --> 16
324
319
  k 6 --> 11 +5
325
320
  l 3 --> 5 +2
326
- total time: 54.2
321
+ total time: 49.7
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -27,16 +27,16 @@ hmm
27
27
  caching input annotation naive seqs in bcrham cache file for 27 clusters (53 seqs)
28
28
  --continue-from-input-partition: using input partition for initial cpath
29
29
  27 clusters (53 seqs)
30
- 27 clusters with 10 procs (0.6s)
31
- 26 clusters with 7 procs (0.6s)
30
+ 27 clusters with 10 procs (0.8s)
31
+ 26 clusters with 7 procs (0.5s)
32
32
  23 clusters with 5 procs (0.5s)
33
33
  22 clusters with 3 procs (0.5s)
34
34
  21 clusters with 2 procs (0.4s)
35
- 21 clusters with 1 proc (0.9s)
36
- partition loop time: 3.5
35
+ 21 clusters with 1 proc (0.8s)
36
+ partition loop time: 3.4
37
37
  getting annotations for final partition
38
- subcluster annotating 18 clusters with steps: (0.8s) (0.4s) (0.3s)
39
- subcluster annotation time 1.5
38
+ subcluster annotating 18 clusters with steps: (0.7s) (0.3s) (0.3s)
39
+ subcluster annotation time 1.4
40
40
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
41
41
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
42
42
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
@@ -47,7 +47,7 @@ getting annotations for final partition
47
47
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
48
48
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
49
49
  warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
50
- total time: 5.3
50
+ total time: 5.0
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
@@ -82,9 +82,9 @@ hmm
82
82
  note not merging entire cpath history
83
83
  partition loop time: 1.8
84
84
  getting annotations for final partition
85
- subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.2s)
86
- subcluster annotation time 1.0
87
- total time: 3.1
85
+ subcluster annotating 6 clusters with steps: (0.5s) (0.2s) (0.1s)
86
+ subcluster annotation time 0.9
87
+ total time: 3.0
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
@@ -115,13 +115,13 @@ hmm
115
115
  reducing n procs to number of clusters: 10 --> 8
116
116
  8 clusters with 8 procs (0.3s)
117
117
  8 clusters with 6 procs (0.3s)
118
- 7 clusters with 4 procs (0.2s)
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
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)
124
+ subcluster annotating 3 clusters with steps: (0.3s) (0.2s) (0.2s)
125
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
@@ -129,7 +129,7 @@ getting annotations for final partition
129
129
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
130
130
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
131
131
  warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
132
- total time: 2.4
132
+ total time: 2.3
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: v1.0.10
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: (0.7s) (0.3s)
183
- subcluster annotation time 1.0
181
+ subcluster annotating 15 clusters with steps: (0.5s) (0.3s)
182
+ subcluster annotation time 0.8
184
183
  total time: 1.1
185
184
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.10
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
@@ -191,7 +189,7 @@ 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
@@ -199,7 +197,7 @@ smith-waterman
199
197
  hmm
200
198
  subcluster annotating 15 clusters with steps: (0.5s) (0.2s)
201
199
  subcluster annotation time 0.7
202
- total time: 0.9
200
+ total time: 1.0
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
205
203
  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
@@ -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: v1.0.10
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
@@ -242,11 +239,10 @@ smith-waterman
242
239
  kept 11 (0.579) unproductive
243
240
  water time: 0.0
244
241
  hmm
245
- subcluster annotating 6 clusters with steps: (0.5s) (0.3s) (0.3s)
246
- subcluster annotation time 1.1
242
+ subcluster annotating 6 clusters with steps: (0.4s) (0.3s) (0.3s)
243
+ subcluster annotation time 1.0
247
244
  total time: 1.2
248
245
  need to get annotations for 6/6 joint igl clusters
249
- tag: v1.0.10
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
@@ -260,7 +256,7 @@ 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: (0.3s) (0.2s) (0.2s)
259
+ subcluster annotating 6 clusters with steps: (0.3s) (0.1s) (0.2s)
264
260
  subcluster annotation time 0.7
265
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
@@ -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: 33.3
275
+ total time: 29.8