partis-bcr 1.0.12.post1.dev2__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev4__cp312-cp312-manylinux1_x86_64.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 (56) hide show
  1. packages/bpp/lib/libbpp-core.a +0 -0
  2. packages/bpp/lib/libbpp-core.so +0 -0
  3. packages/bpp/lib/libbpp-core.so.2 +0 -0
  4. packages/bpp/lib/libbpp-core.so.2.0.3 +0 -0
  5. packages/bpp/lib/libbpp-phyl.a +0 -0
  6. packages/bpp/lib/libbpp-phyl.so +0 -0
  7. packages/bpp/lib/libbpp-phyl.so.9 +0 -0
  8. packages/bpp/lib/libbpp-phyl.so.9.1.3 +0 -0
  9. packages/bpp/lib/libbpp-seq.a +0 -0
  10. packages/bpp/lib/libbpp-seq.so +0 -0
  11. packages/bpp/lib/libbpp-seq.so.9 +0 -0
  12. packages/bpp/lib/libbpp-seq.so.9.1.3 +0 -0
  13. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/METADATA +1 -1
  14. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/RECORD +56 -44
  15. test/new-results/partition-new-simu/fasttree/iclust-0/log +2 -2
  16. test/new-results/run-times.csv +6 -6
  17. test/new-results/test.log +17 -17
  18. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +1 -1
  19. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
  20. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
  21. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  22. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  23. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  24. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  25. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  26. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  27. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  28. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  29. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  30. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  31. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  32. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  36. test/paired/new-results/run-times.csv +7 -7
  37. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +5 -5
  38. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +5 -5
  39. test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -4
  40. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  41. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  42. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  43. test/paired/new-results/test.log +74 -74
  44. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-alleles.py +0 -0
  45. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/cf-germlines.py +0 -0
  46. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/compare-plotdirs.py +0 -0
  47. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/extract-pairing-info.py +0 -0
  48. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/gctree-run.py +0 -0
  49. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/get-naive-probabilities.py +0 -0
  50. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/parse-output.py +0 -0
  51. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/partis-test.py +0 -0
  52. {partis_bcr-1.0.12.post1.dev2.data → partis_bcr-1.0.12.post1.dev4.data}/scripts/split-loci.py +0 -0
  53. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/WHEEL +0 -0
  54. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/entry_points.txt +0 -0
  55. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/licenses/COPYING +0 -0
  56. {partis_bcr-1.0.12.post1.dev2.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/top_level.txt +0 -0
test/paired/new-results/test.log CHANGED
@@ -21,19 +21,19 @@ smith-waterman (writing parameters)
21
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  kept 25 (0.446) unproductive
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  writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
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  writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
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- water time: 0.7 (ig-sw 0.7 processing 0.0)
24
+ water time: 0.7 (ig-sw 0.6 processing 0.0)
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  writing hmms removed 16 genes from glfo (leaving v 6 d 18 j 4)
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- (0.6 sec)
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+ (0.5 sec)
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  hmm
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  reading output
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  read 56 hmm output lines with 56 sequences in 56 events (0 failures)
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  writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
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- writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
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+ writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
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  infra time: 1.1
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- hmm step time: 2.2
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+ hmm step time: 2.1
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  writing hmms removed 3 genes from glfo (leaving v 6 d 15 j 4)
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- (0.4 sec)
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- total time: 4.0
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+ (0.3 sec)
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+ total time: 3.9
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  cache-parameters igk:
38
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  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
39
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  run partis cache-parameters --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -98,13 +98,13 @@ hmm
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  reading output
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  read 21 hmm output lines with 21 sequences in 21 events (0 failures)
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  writing parameters to test/paired/new-results/test/parameters/simu/igl/hmm (0.3 sec)
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- writing parameters to test/paired/new-results/test/parameters/simu/igl/true (0.3 sec)
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- infra time: 0.6
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+ writing parameters to test/paired/new-results/test/parameters/simu/igl/true (0.2 sec)
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+ infra time: 0.5
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  hmm step time: 0.9
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  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
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  (0.1 sec)
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- total time: 1.7
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- total time: 12.4
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+ total time: 1.6
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+ total time: 12.0
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  partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu
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  warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
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  partition igh:
@@ -124,11 +124,11 @@ smith-waterman
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  hmm
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  caching all 56 naive sequences (1.0s)
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  collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
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- 50 clusters with 10 procs (0.6s)
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+ 50 clusters with 10 procs (0.5s)
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  44 clusters with 7 procs (0.5s)
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  36 clusters with 5 procs (0.4s)
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  31 clusters with 3 procs (0.3s)
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- 29 clusters with 2 procs (0.5s)
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+ 29 clusters with 2 procs (0.4s)
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  23 clusters with 1 proc (0.6s)
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  note not merging entire cpath history
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  partition loop time: 2.8
@@ -137,8 +137,8 @@ getting annotations for final partition
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  warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
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  (0.0 sec)
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- subcluster annotation time 1.0
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- total time: 5.0
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+ subcluster annotation time 0.9
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+ total time: 4.9
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  partition igk:
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  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
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  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igk --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -164,7 +164,7 @@ hmm
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  getting annotations for final partition
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  subcluster annotating 6 clusters with steps: (0.3s) (0.1s) (0.1s) plotting performance (0.0 sec)
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- subcluster annotation time 0.5
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+ subcluster annotation time 0.4
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  total time: 1.5
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  partition igl:
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  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -260,7 +260,7 @@ smith-waterman
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  hmm
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  subcluster annotating 15 clusters with steps: (0.3s) (0.1s)
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  subcluster annotation time 0.4
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- total time: 0.5
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+ total time: 0.4
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  igh+igl: synchronizing heavy and light chain cluster paths
265
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  removing badly + unpaired seqs: kept 7 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 3 l 4
266
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  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
@@ -331,7 +331,7 @@ hmm
331
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  h 20 --> 23 +3
332
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  k 6 --> 15 +9
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  l 3 --> 8 +5
334
- total time: 20.5
334
+ total time: 19.7
335
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  subset-partition-new-simu partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
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  note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
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  --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -362,7 +362,7 @@ hmm
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  merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
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  run partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --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 --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
364
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  log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
365
- total time: 70.3
365
+ total time: 67.9
366
366
  seed-partition-new-simu partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
367
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  removing seqs very different from seed seq
368
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  wrong/no removed singly kept missing
@@ -400,7 +400,7 @@ getting annotations for final partition
400
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  reading output
401
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  read 12 hmm output lines with 17 sequences in 12 events (0 failures)
402
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  hmm step time: 0.3
403
- total time: 2.0
403
+ total time: 1.9
404
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  partition igk:
405
405
  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
406
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  run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -423,7 +423,7 @@ hmm
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  getting annotations for final partition
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  subcluster annotating 2 clusters with steps: (0.1s) (0.1s) (0.1s)
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  subcluster annotation time 0.2
426
- total time: 0.7
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+ total time: 0.6
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  partition igl:
428
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  note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
429
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  run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igl.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -552,7 +552,7 @@ hmm
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  N clusters with all seqs:
553
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  h 12 --> 1 -11
554
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  k 2 --> 1 -1
555
- total time: 9.7
555
+ total time: 9.2
556
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  get-selection-metrics-new-simu partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
557
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  get-selection-metrics igh+igk: igh
558
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  run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -673,10 +673,10 @@ hmm
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  skipped 1/4 clusters that had no uids in common with tree
674
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  writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
675
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  writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
676
- total time: 5.8
676
+ total time: 5.5
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  cache-parameters-data partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
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  note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
679
- run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/929072/meta.yaml --n-max-queries 100
679
+ run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/859198/meta.yaml --n-max-queries 100
680
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  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
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  extract_pairing_info(): read 100 sequences with 48 droplet ids
682
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  droplet id separators (set automatically): _ indices: [0]
@@ -687,9 +687,9 @@ hmm
687
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  2 42 0.875
688
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  3 2 0.042
689
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  4 2 0.042
690
- run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/929072 --input-metafname /tmp/runner/hmms/929072/meta.yaml --n-max-queries 100
690
+ run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/859198 --input-metafname /tmp/runner/hmms/859198/meta.yaml --n-max-queries 100
691
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  --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
692
- --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
692
+ --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/859198/meta.yaml: paired-uids
693
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  read pairing info for 100 seqs from input meta file
694
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  running vsearch on 100 sequences:
695
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  igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -712,10 +712,10 @@ totals: igh 48 igk 37 igl 15
712
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  2 0.13 h l
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  1 0.07 h k
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  1 0.07 h h k
715
- writing to /tmp/runner/hmms/929072/
716
- igh: 48 to 929072/igh.fa
717
- igk: 37 to 929072/igk.fa
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- igl: 15 to 929072/igl.fa
715
+ writing to /tmp/runner/hmms/859198/
716
+ igh: 48 to 859198/igh.fa
717
+ igk: 37 to 859198/igk.fa
718
+ igl: 15 to 859198/igl.fa
719
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  writing to paired subdirs
720
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  igh+igk:
721
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  igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +724,8 @@ writing to paired subdirs
724
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  igh: 15 / 48 to igh+igl/igh.fa
725
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  igl: 15 / 15 to igh+igl/igl.fa
726
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  cache-parameters igh:
727
- run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/929072/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/929072/meta.yaml
728
- --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
727
+ run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/859198/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/859198/meta.yaml
728
+ --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/859198/meta.yaml: paired-uids
729
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  caching parameters
730
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  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
731
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  keeping 23 / 198 v genes
@@ -744,7 +744,7 @@ smith-waterman (writing parameters)
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  writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.0 sec)
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  water time: 2.2 (ig-sw 2.1 processing 0.1)
746
746
  writing hmms removed 13 genes from glfo (leaving v 23 d 19 j 6)
747
- (1.0 sec)
747
+ (0.9 sec)
748
748
  hmm
749
749
  reading output
750
750
  read 48 hmm output lines with 48 sequences in 48 events (0 failures)
@@ -752,11 +752,11 @@ hmm
752
752
  infra time: 2.0
753
753
  hmm step time: 3.0
754
754
  writing hmms removed 1 genes from glfo (leaving v 23 d 18 j 6)
755
- (1.0 sec)
756
- total time: 7.6
755
+ (0.9 sec)
756
+ total time: 7.3
757
757
  cache-parameters igk:
758
- run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/929072/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/929072/meta.yaml
759
- --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
758
+ run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/859198/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/859198/meta.yaml
759
+ --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/859198/meta.yaml: paired-uids
760
760
  caching parameters
761
761
  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
762
762
  keeping 16 / 64 v genes
@@ -784,10 +784,10 @@ hmm
784
784
  hmm step time: 1.9
785
785
  writing hmms removed 0 genes from glfo (leaving v 16 d 1 j 7)
786
786
  (1.0 sec)
787
- total time: 5.7
787
+ total time: 5.6
788
788
  cache-parameters igl:
789
- run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/929072/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/929072/meta.yaml
790
- --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
789
+ run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/859198/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/859198/meta.yaml
790
+ --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/859198/meta.yaml: paired-uids
791
791
  caching parameters
792
792
  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
793
793
  keeping 10 / 80 v genes
@@ -801,7 +801,7 @@ smith-waterman (writing parameters)
801
801
  running 10 procs for 15 seqs
802
802
  info for 15 / 15 = 1.000 (removed: 0 failed)
803
803
  writing sw results to test/paired/new-results/test/parameters/data/igl/sw-cache.yaml
804
- writing parameters to test/paired/new-results/test/parameters/data/igl/sw (0.9 sec)
804
+ writing parameters to test/paired/new-results/test/parameters/data/igl/sw (0.8 sec)
805
805
  water time: 0.9 (ig-sw 0.9 processing 0.0)
806
806
  writing hmms removed 6 genes from glfo (leaving v 10 d 1 j 3)
807
807
  (0.6 sec)
@@ -813,9 +813,9 @@ hmm
813
813
  hmm step time: 1.1
814
814
  writing hmms removed 0 genes from glfo (leaving v 10 d 1 j 3)
815
815
  (0.6 sec)
816
- total time: 3.5
817
- warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/929072/: failed.fa
818
- total time: 22.1
816
+ total time: 3.4
817
+ warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/859198/: failed.fa
818
+ total time: 21.5
819
819
  simulate partis simulate --dont-write-git-info --paired-loci --parameter-dir test/paired/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/test/simu --indel-frequency 0.2
820
820
  igh+igk: simulating 7 events
821
821
  warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
@@ -825,110 +825,110 @@ hmm
825
825
  simulating
826
826
  --> proc 0
827
827
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
828
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-0.nwk
828
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/416305/trees-sub-0.nwk
829
829
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
830
830
  made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
831
831
  total time: 0.2
832
832
 
833
833
  --> proc 1
834
834
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
835
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-1.nwk
835
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/416305/trees-sub-1.nwk
836
836
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
837
- made 1 event with 8 seqs in 0.2s (0.1s of which was running bppseqgen)
837
+ made 1 event with 8 seqs in 0.2s (0.0s of which was running bppseqgen)
838
838
  total time: 0.3
839
839
 
840
840
  --> proc 2
841
841
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
842
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-2.nwk
842
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/416305/trees-sub-2.nwk
843
843
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
844
844
  made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
845
845
  total time: 0.1
846
846
 
847
847
  --> proc 3
848
848
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
849
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-3.nwk
849
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/416305/trees-sub-3.nwk
850
850
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
851
- made 1 event with 6 seqs in 0.2s (0.0s of which was running bppseqgen)
851
+ made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
852
852
  total time: 0.3
853
853
 
854
854
  --> proc 4
855
855
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
856
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-4.nwk
856
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/416305/trees-sub-4.nwk
857
857
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
858
- made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
858
+ made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
859
859
  total time: 0.2
860
860
 
861
861
  --> proc 5
862
862
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
863
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-5.nwk
863
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/416305/trees-sub-5.nwk
864
864
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
865
865
  made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
866
866
  total time: 0.2
867
867
 
868
868
  --> proc 6
869
869
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
870
- resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/702692/trees-sub-6.nwk
870
+ resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/416305/trees-sub-6.nwk
871
871
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
872
872
  made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
873
873
  total time: 0.2
874
874
 
875
875
  read 7 events with 40 seqs from 7 .yaml files
876
- total time: 4.3
876
+ total time: 4.0
877
877
  simulate igh+igk: igk
878
878
  run partis simulate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igk --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 2077655082 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igk.yaml
879
879
  note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
880
880
  simulating
881
881
  --> proc 0
882
882
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
883
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-0.nwk
883
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/92242/trees-sub-0.nwk
884
884
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
885
- made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
886
- total time: 0.1
885
+ made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
886
+ total time: 0.2
887
887
 
888
888
  --> proc 1
889
889
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
890
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-1.nwk
890
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/92242/trees-sub-1.nwk
891
891
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
892
892
  made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
893
893
  total time: 0.2
894
894
 
895
895
  --> proc 2
896
896
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
897
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-2.nwk
897
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/92242/trees-sub-2.nwk
898
898
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
899
899
  made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
900
900
  total time: 0.1
901
901
 
902
902
  --> proc 3
903
903
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
904
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-3.nwk
904
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/92242/trees-sub-3.nwk
905
905
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
906
906
  made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
907
907
  total time: 0.1
908
908
 
909
909
  --> proc 4
910
910
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
911
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-4.nwk
911
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/92242/trees-sub-4.nwk
912
912
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
913
913
  made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
914
914
  total time: 0.1
915
915
 
916
916
  --> proc 5
917
917
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
918
- resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-5.nwk
918
+ resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/92242/trees-sub-5.nwk
919
919
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
920
920
  made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
921
- total time: 0.2
921
+ total time: 0.1
922
922
 
923
923
  --> proc 6
924
924
  reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
925
- resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/224927/trees-sub-6.nwk
925
+ resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/92242/trees-sub-6.nwk
926
926
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
927
927
  made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
928
928
  total time: 0.2
929
929
 
930
930
  read 7 events with 40 seqs from 7 .yaml files
931
- total time: 4.1
931
+ total time: 4.0
932
932
  igh+igl: simulating 3 events
933
933
  warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
934
934
  simulate igh+igl: igh
@@ -937,54 +937,54 @@ simulating
937
937
  simulating
938
938
  --> proc 0
939
939
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
940
- resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/894275/trees-sub-0.nwk
940
+ resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/701697/trees-sub-0.nwk
941
941
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
942
942
  made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
943
943
  total time: 0.2
944
944
 
945
945
  --> proc 1
946
946
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
947
- resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/894275/trees-sub-1.nwk
947
+ resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/701697/trees-sub-1.nwk
948
948
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
949
949
  made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
950
950
  total time: 0.1
951
951
 
952
952
  --> proc 2
953
953
  reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
954
- resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/894275/trees-sub-2.nwk
954
+ resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/701697/trees-sub-2.nwk
955
955
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
956
956
  made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
957
957
  total time: 0.1
958
958
 
959
959
  read 3 events with 13 seqs from 3 .yaml files
960
- total time: 2.1
960
+ total time: 2.0
961
961
  simulate igh+igl: igl
962
962
  run partis simulate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igl --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1083609742 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igl.yaml
963
963
  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
964
964
  simulating
965
965
  --> proc 0
966
966
  reco params: test/paired/new-results/test/parameters/data/igl/hmm shm params: test/paired/new-results/test/parameters/data/igl/hmm
967
- resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/883242/trees-sub-0.nwk
967
+ resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/654474/trees-sub-0.nwk
968
968
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
969
969
  made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
970
970
  total time: 0.1
971
971
 
972
972
  --> proc 1
973
973
  reco params: test/paired/new-results/test/parameters/data/igl/hmm shm params: test/paired/new-results/test/parameters/data/igl/hmm
974
- resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/883242/trees-sub-1.nwk
974
+ resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/654474/trees-sub-1.nwk
975
975
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
976
976
  made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
977
977
  total time: 0.1
978
978
 
979
979
  --> proc 2
980
980
  reco params: test/paired/new-results/test/parameters/data/igl/hmm shm params: test/paired/new-results/test/parameters/data/igl/hmm
981
- resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/883242/trees-sub-2.nwk
981
+ resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/654474/trees-sub-2.nwk
982
982
  using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
983
983
  made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
984
984
  total time: 0.1
985
985
 
986
986
  read 3 events with 13 seqs from 3 .yaml files
987
- total time: 2.1
987
+ total time: 2.0
988
988
  igh+igk: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
989
989
  igh+igl: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
990
990
  concatenating heavy chain loci:
@@ -997,4 +997,4 @@ simulating
997
997
  apportioned 106 seqs among 42 droplets (mean/2 1.3): 2 2 2 4 4 2 4 4 4 4 2 2 2 4 2 2 2 2 2 2 2 2 2 2 4 2 4 2 2 2 2 2 4 4 2 2 2 2 2 2 2 2
998
998
  removed 15 / 106 = 0.14 seqs from outfos (leaving 9 / 91 unpaired)
999
999
  writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
1000
- total time: 17.8
1000
+ total time: 16.9