partis-bcr 1.0.12.post1.dev4__cp312-cp312-manylinux1_x86_64.whl → 1.0.13__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-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/RECORD +45 -45
- test/new-results/partition-new-simu/fasttree/iclust-0/log +2 -2
- test/new-results/partition-new-simu/fasttree/iclust-2/log +1 -1
- test/new-results/run-times.csv +9 -9
- test/new-results/test.log +23 -23
- 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/igh+igk/partition-igh/fasttree/iclust-1/log +1 -1
- test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
- test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
- test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
- test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
- test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
- test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
- test/paired/new-results/run-times.csv +7 -7
- test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +13 -9
- test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +14 -10
- test/paired/new-results/subset-partition-new-simu/merged-partition.log +10 -6
- 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 +112 -103
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/cf-alleles.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/cf-germlines.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/compare-plotdirs.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/extract-pairing-info.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/gctree-run.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/get-naive-probabilities.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/parse-output.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/partis-test.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/split-loci.py +0 -0
- {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/WHEEL +0 -0
- {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/entry_points.txt +0 -0
- {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/licenses/COPYING +0 -0
- {partis_bcr-1.0.12.post1.dev4.dist-info → partis_bcr-1.0.13.dist-info}/top_level.txt +0 -0
test/paired/new-results/test.log
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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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[91mrun[0m partis cache-parameters --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/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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[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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|
818
|
-
total time:
|
|
824
|
+
(0.7 sec)
|
|
825
|
+
total time: 3.6
|
|
826
|
+
[93mwarning[0m expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/294229/: failed.fa
|
|
827
|
+
total time: 23.2
|
|
819
828
|
[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
|
|
820
829
|
[94migh+igk[0m: simulating 7 events
|
|
821
830
|
[93mwarning[0m drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
|
|
@@ -825,110 +834,110 @@ hmm
|
|
|
825
834
|
simulating
|
|
826
835
|
--> proc 0
|
|
827
836
|
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/
|
|
837
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/95313/trees-sub-0.nwk
|
|
829
838
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
830
839
|
made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
|
|
831
840
|
total time: 0.2
|
|
832
841
|
|
|
833
842
|
--> proc 1
|
|
834
843
|
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/
|
|
844
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/95313/trees-sub-1.nwk
|
|
836
845
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
837
|
-
made 1 event with 8 seqs in 0.2s (0.
|
|
846
|
+
made 1 event with 8 seqs in 0.2s (0.1s of which was running bppseqgen)
|
|
838
847
|
total time: 0.3
|
|
839
848
|
|
|
840
849
|
--> proc 2
|
|
841
850
|
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/
|
|
851
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/95313/trees-sub-2.nwk
|
|
843
852
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
844
|
-
made 1 event with 1 seqs in 0.
|
|
853
|
+
made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
845
854
|
total time: 0.1
|
|
846
855
|
|
|
847
856
|
--> proc 3
|
|
848
857
|
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/
|
|
858
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/95313/trees-sub-3.nwk
|
|
850
859
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
851
860
|
made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
852
|
-
total time: 0.
|
|
861
|
+
total time: 0.2
|
|
853
862
|
|
|
854
863
|
--> proc 4
|
|
855
864
|
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/
|
|
865
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/95313/trees-sub-4.nwk
|
|
857
866
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
858
|
-
made 1 event with 1 seqs in 0.
|
|
859
|
-
total time: 0.
|
|
867
|
+
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
868
|
+
total time: 0.1
|
|
860
869
|
|
|
861
870
|
--> proc 5
|
|
862
871
|
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/
|
|
872
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/95313/trees-sub-5.nwk
|
|
864
873
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
865
874
|
made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
866
|
-
total time: 0.
|
|
875
|
+
total time: 0.1
|
|
867
876
|
|
|
868
877
|
--> proc 6
|
|
869
878
|
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/
|
|
879
|
+
resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/95313/trees-sub-6.nwk
|
|
871
880
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
872
881
|
made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
|
|
873
882
|
total time: 0.2
|
|
874
883
|
|
|
875
884
|
read 7 events with 40 seqs from 7 .yaml files
|
|
876
|
-
total time: 4.
|
|
885
|
+
total time: 4.4
|
|
877
886
|
[44msimulate[0m [94migh+igk[0m:[94m igk[0m
|
|
878
887
|
[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
|
|
879
888
|
note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
|
|
880
889
|
simulating
|
|
881
890
|
--> proc 0
|
|
882
891
|
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/
|
|
892
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/464807/trees-sub-0.nwk
|
|
884
893
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
885
894
|
made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
|
|
886
895
|
total time: 0.2
|
|
887
896
|
|
|
888
897
|
--> proc 1
|
|
889
898
|
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/
|
|
899
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/464807/trees-sub-1.nwk
|
|
891
900
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
892
901
|
made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
893
902
|
total time: 0.2
|
|
894
903
|
|
|
895
904
|
--> proc 2
|
|
896
905
|
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/
|
|
906
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/464807/trees-sub-2.nwk
|
|
898
907
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
899
|
-
made 1 event with 1 seqs in 0.
|
|
900
|
-
total time: 0.
|
|
908
|
+
made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
909
|
+
total time: 0.2
|
|
901
910
|
|
|
902
911
|
--> proc 3
|
|
903
912
|
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/
|
|
913
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/464807/trees-sub-3.nwk
|
|
905
914
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
906
915
|
made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
907
|
-
total time: 0.
|
|
916
|
+
total time: 0.2
|
|
908
917
|
|
|
909
918
|
--> proc 4
|
|
910
919
|
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/
|
|
920
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/464807/trees-sub-4.nwk
|
|
912
921
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
913
|
-
made 1 event with 1 seqs in 0.
|
|
914
|
-
total time: 0.
|
|
922
|
+
made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
923
|
+
total time: 0.2
|
|
915
924
|
|
|
916
925
|
--> proc 5
|
|
917
926
|
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/
|
|
927
|
+
resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/464807/trees-sub-5.nwk
|
|
919
928
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
920
929
|
made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
921
|
-
total time: 0.
|
|
930
|
+
total time: 0.2
|
|
922
931
|
|
|
923
932
|
--> proc 6
|
|
924
933
|
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/
|
|
934
|
+
resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/464807/trees-sub-6.nwk
|
|
926
935
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
927
|
-
made 1 event with 13 seqs in 0.1s (0.
|
|
936
|
+
made 1 event with 13 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
928
937
|
total time: 0.2
|
|
929
938
|
|
|
930
939
|
read 7 events with 40 seqs from 7 .yaml files
|
|
931
|
-
total time: 4.
|
|
940
|
+
total time: 4.3
|
|
932
941
|
[94migh+igl[0m: simulating 3 events
|
|
933
942
|
[93mwarning[0m drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
|
|
934
943
|
[44msimulate[0m [94migh+igl[0m:[94m igh[0m
|
|
@@ -937,54 +946,54 @@ simulating
|
|
|
937
946
|
simulating
|
|
938
947
|
--> proc 0
|
|
939
948
|
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/
|
|
949
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/945409/trees-sub-0.nwk
|
|
941
950
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
942
951
|
made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
|
|
943
|
-
total time: 0.
|
|
952
|
+
total time: 0.1
|
|
944
953
|
|
|
945
954
|
--> proc 1
|
|
946
955
|
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/
|
|
956
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/945409/trees-sub-1.nwk
|
|
948
957
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
949
958
|
made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
950
959
|
total time: 0.1
|
|
951
960
|
|
|
952
961
|
--> proc 2
|
|
953
962
|
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/
|
|
963
|
+
resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/945409/trees-sub-2.nwk
|
|
955
964
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
956
965
|
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
957
966
|
total time: 0.1
|
|
958
967
|
|
|
959
968
|
read 3 events with 13 seqs from 3 .yaml files
|
|
960
|
-
total time: 2.
|
|
969
|
+
total time: 2.2
|
|
961
970
|
[44msimulate[0m [94migh+igl[0m:[94m igl[0m
|
|
962
971
|
[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
|
|
963
972
|
note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
|
|
964
973
|
simulating
|
|
965
974
|
--> proc 0
|
|
966
975
|
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/
|
|
976
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/73193/trees-sub-0.nwk
|
|
968
977
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
969
978
|
made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
970
979
|
total time: 0.1
|
|
971
980
|
|
|
972
981
|
--> proc 1
|
|
973
982
|
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/
|
|
983
|
+
resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/73193/trees-sub-1.nwk
|
|
975
984
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
976
985
|
made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
977
986
|
total time: 0.1
|
|
978
987
|
|
|
979
988
|
--> proc 2
|
|
980
989
|
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/
|
|
990
|
+
resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/73193/trees-sub-2.nwk
|
|
982
991
|
using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
|
|
983
992
|
made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
|
|
984
993
|
total time: 0.1
|
|
985
994
|
|
|
986
995
|
read 3 events with 13 seqs from 3 .yaml files
|
|
987
|
-
total time: 2.
|
|
996
|
+
total time: 2.2
|
|
988
997
|
[94migh+igk[0m: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
|
|
989
998
|
[94migh+igl[0m: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
|
|
990
999
|
concatenating heavy chain loci:
|
|
@@ -997,4 +1006,4 @@ simulating
|
|
|
997
1006
|
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
1007
|
removed 15 / 106 = 0.14 seqs from outfos (leaving 9 / 91 unpaired)
|
|
999
1008
|
writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
|
|
1000
|
-
total time:
|
|
1009
|
+
total time: 18.6
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
{partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.data}/scripts/extract-pairing-info.py
RENAMED
|
File without changes
|
|
File without changes
|
{partis_bcr-1.0.12.post1.dev4.data → partis_bcr-1.0.13.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
|