partis-bcr 1.0.13__cp312-cp312-manylinux1_x86_64.whl → 1.0.13.post1.dev2__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.
- {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/RECORD +47 -47
- python/processargs.py +4 -1
- test/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
- test/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
- test/new-results/run-times.csv +7 -7
- test/new-results/test.log +12 -12
- test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +3 -3
- test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +4 -4
- test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
- test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +2 -2
- test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +108 -108
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +84 -84
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +62 -62
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +19 -19
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +25 -25
- test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +36 -36
- test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +23 -23
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +46 -46
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +46 -46
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +46 -46
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +16 -16
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +16 -16
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +48 -48
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +49 -49
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +28 -28
- test/paired/new-results/run-times.csv +7 -7
- test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +6 -10
- test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +10 -14
- test/paired/new-results/subset-partition-new-simu/merged-partition.log +4 -8
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
- test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
- test/paired/new-results/test.log +84 -93
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/cf-alleles.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/partis-test.py +0 -0
- {partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/entry_points.txt +0 -0
- {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/licenses/COPYING +0 -0
- {partis_bcr-1.0.13.dist-info → partis_bcr-1.0.13.post1.dev2.dist-info}/top_level.txt +0 -0
test/paired/new-results/test.log
CHANGED
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hmm step time: 2.2
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[91mrun[0m 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
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writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.4 sec)
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[92mpartition-new-simu[0m 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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[93mwarning[0m ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
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hmm
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caching all 56 naive sequences (1.1s)
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collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
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subcluster annotating 20 clusters with steps: (0.7s) (0.2s) plotting performance
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[93mwarning[0m skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
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[91mrun[0m 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
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[91mrun[0m partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igl --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/partition-new-simu/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
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[92mseed-partition-new-simu[0m 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
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[91mrun[0m 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
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[91mrun[0m 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
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[92mget-selection-metrics-new-simu[0m 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
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[91mrun[0m 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
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total time:
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extract_pairing_info(): read 100 sequences with 48 droplet ids
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@@ -696,9 +687,9 @@ hmm
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--input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/
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igh: 49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
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@@ -721,10 +712,10 @@ totals: igh 48 igk 37 igl 15
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[91mrun[0m partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/742655/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/742655/meta.yaml
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--input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/742655/meta.yaml: paired-uids
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@@ -759,13 +750,13 @@ hmm
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--input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/
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[91mrun[0m partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/742655/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/742655/meta.yaml
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--input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/742655/meta.yaml: paired-uids
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vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
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@@ -781,22 +772,22 @@ smith-waterman (writing parameters)
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info for 37 / 37 = 1.000 (removed: 0 failed)
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water time: 1.5 (ig-sw 1.4 processing 0.1)
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[91mrun[0m partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/742655/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/742655/meta.yaml
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@@ -813,18 +804,18 @@ smith-waterman (writing parameters)
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total time: 21.9
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[92msimulate[0m 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
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|
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simulating
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--> proc 0
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|
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resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
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resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/969229/trees-sub-0.nwk
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--> proc 1
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|
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resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
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resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/969229/trees-sub-1.nwk
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total time: 0.
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total time: 0.2
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--> proc 2
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|
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|
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resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
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+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/969229/trees-sub-2.nwk
|
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using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
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total time: 0.
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|
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|
--> proc 3
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|
|
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|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
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|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/969229/trees-sub-3.nwk
|
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using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
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|
made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
|
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total time: 0.2
|
|
862
853
|
|
|
863
854
|
--> proc 4
|
|
864
855
|
reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
|
|
865
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
856
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/969229/trees-sub-4.nwk
|
|
866
857
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
867
858
|
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
868
859
|
total time: 0.1
|
|
869
860
|
|
|
870
861
|
--> proc 5
|
|
871
862
|
reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
|
|
872
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
863
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/969229/trees-sub-5.nwk
|
|
873
864
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
874
865
|
made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
875
|
-
total time: 0.
|
|
866
|
+
total time: 0.2
|
|
876
867
|
|
|
877
868
|
--> proc 6
|
|
878
869
|
reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
|
|
879
|
-
resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/
|
|
870
|
+
resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/969229/trees-sub-6.nwk
|
|
880
871
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
881
|
-
made 1 event with 13 seqs in 0.
|
|
882
|
-
total time: 0.
|
|
872
|
+
made 1 event with 13 seqs in 0.2s (0.1s of which was running bppseqgen)
|
|
873
|
+
total time: 0.3
|
|
883
874
|
|
|
884
875
|
read 7 events with 40 seqs from 7 .yaml files
|
|
885
|
-
total time: 4.
|
|
876
|
+
total time: 4.2
|
|
886
877
|
[44msimulate[0m [94migh+igk[0m:[94m igk[0m
|
|
887
878
|
[91mrun[0m 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
|
|
888
879
|
note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
|
|
889
880
|
simulating
|
|
890
881
|
--> proc 0
|
|
891
882
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
892
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
883
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/39721/trees-sub-0.nwk
|
|
893
884
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
894
885
|
made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
|
|
895
886
|
total time: 0.2
|
|
896
887
|
|
|
897
888
|
--> proc 1
|
|
898
889
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
899
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
890
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/39721/trees-sub-1.nwk
|
|
900
891
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
901
892
|
made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
902
893
|
total time: 0.2
|
|
903
894
|
|
|
904
895
|
--> proc 2
|
|
905
896
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
906
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
897
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/39721/trees-sub-2.nwk
|
|
907
898
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
908
|
-
made 1 event with 1 seqs in 0.
|
|
909
|
-
total time: 0.
|
|
899
|
+
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
900
|
+
total time: 0.1
|
|
910
901
|
|
|
911
902
|
--> proc 3
|
|
912
903
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
913
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
904
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/39721/trees-sub-3.nwk
|
|
914
905
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
915
906
|
made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
916
907
|
total time: 0.2
|
|
917
908
|
|
|
918
909
|
--> proc 4
|
|
919
910
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
920
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
911
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/39721/trees-sub-4.nwk
|
|
921
912
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
922
|
-
made 1 event with 1 seqs in 0.
|
|
913
|
+
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
923
914
|
total time: 0.2
|
|
924
915
|
|
|
925
916
|
--> proc 5
|
|
926
917
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
927
|
-
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/
|
|
918
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/39721/trees-sub-5.nwk
|
|
928
919
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
929
|
-
made 1 event with 1 seqs in 0.
|
|
920
|
+
made 1 event with 1 seqs in 0.2s (0.0s of which was running bppseqgen)
|
|
930
921
|
total time: 0.2
|
|
931
922
|
|
|
932
923
|
--> proc 6
|
|
933
924
|
reco params: test/paired/new-results/test/parameters/data/igk/hmm shm params: test/paired/new-results/test/parameters/data/igk/hmm
|
|
934
|
-
resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/
|
|
925
|
+
resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/39721/trees-sub-6.nwk
|
|
935
926
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
936
|
-
made 1 event with 13 seqs in 0.1s (0.
|
|
927
|
+
made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
|
|
937
928
|
total time: 0.2
|
|
938
929
|
|
|
939
930
|
read 7 events with 40 seqs from 7 .yaml files
|
|
940
|
-
total time: 4.
|
|
931
|
+
total time: 4.1
|
|
941
932
|
[94migh+igl[0m: simulating 3 events
|
|
942
933
|
[93mwarning[0m drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
|
|
943
934
|
[44msimulate[0m [94migh+igl[0m:[94m igh[0m
|
|
@@ -946,54 +937,54 @@ simulating
|
|
|
946
937
|
simulating
|
|
947
938
|
--> proc 0
|
|
948
939
|
reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
|
|
949
|
-
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/
|
|
940
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/857076/trees-sub-0.nwk
|
|
950
941
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
951
942
|
made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
952
|
-
total time: 0.
|
|
943
|
+
total time: 0.2
|
|
953
944
|
|
|
954
945
|
--> proc 1
|
|
955
946
|
reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
|
|
956
|
-
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/
|
|
947
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/857076/trees-sub-1.nwk
|
|
957
948
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
958
949
|
made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
959
950
|
total time: 0.1
|
|
960
951
|
|
|
961
952
|
--> proc 2
|
|
962
953
|
reco params: test/paired/new-results/test/parameters/data/igh/hmm shm params: test/paired/new-results/test/parameters/data/igh/hmm
|
|
963
|
-
resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/
|
|
954
|
+
resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/857076/trees-sub-2.nwk
|
|
964
955
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
965
956
|
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
966
957
|
total time: 0.1
|
|
967
958
|
|
|
968
959
|
read 3 events with 13 seqs from 3 .yaml files
|
|
969
|
-
total time: 2.
|
|
960
|
+
total time: 2.0
|
|
970
961
|
[44msimulate[0m [94migh+igl[0m:[94m igl[0m
|
|
971
962
|
[91mrun[0m 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
|
|
972
963
|
note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
|
|
973
964
|
simulating
|
|
974
965
|
--> proc 0
|
|
975
966
|
reco params: test/paired/new-results/test/parameters/data/igl/hmm shm params: test/paired/new-results/test/parameters/data/igl/hmm
|
|
976
|
-
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/
|
|
967
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/534188/trees-sub-0.nwk
|
|
977
968
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
978
969
|
made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
979
970
|
total time: 0.1
|
|
980
971
|
|
|
981
972
|
--> proc 1
|
|
982
973
|
reco params: test/paired/new-results/test/parameters/data/igl/hmm shm params: test/paired/new-results/test/parameters/data/igl/hmm
|
|
983
|
-
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/
|
|
974
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/534188/trees-sub-1.nwk
|
|
984
975
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
985
976
|
made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
986
977
|
total time: 0.1
|
|
987
978
|
|
|
988
979
|
--> proc 2
|
|
989
980
|
reco params: test/paired/new-results/test/parameters/data/igl/hmm shm params: test/paired/new-results/test/parameters/data/igl/hmm
|
|
990
|
-
resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/
|
|
981
|
+
resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/534188/trees-sub-2.nwk
|
|
991
982
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
992
983
|
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
993
984
|
total time: 0.1
|
|
994
985
|
|
|
995
986
|
read 3 events with 13 seqs from 3 .yaml files
|
|
996
|
-
total time: 2.
|
|
987
|
+
total time: 2.0
|
|
997
988
|
[94migh+igk[0m: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
|
|
998
989
|
[94migh+igl[0m: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
|
|
999
990
|
concatenating heavy chain loci:
|
|
@@ -1006,4 +997,4 @@ simulating
|
|
|
1006
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
|
|
1007
998
|
removed 15 / 106 = 0.14 seqs from outfos (leaving 9 / 91 unpaired)
|
|
1008
999
|
writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
|
|
1009
|
-
total time:
|
|
1000
|
+
total time: 17.5
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/extract-pairing-info.py
RENAMED
|
File without changes
|
|
File without changes
|
{partis_bcr-1.0.13.data → partis_bcr-1.0.13.post1.dev2.data}/scripts/get-naive-probabilities.py
RENAMED
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|