partis-bcr 1.0.12__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev2__cp312-cp312-manylinux1_x86_64.whl

test/paired/new-results/test.log

@@ -28,12 +28,12 @@ hmm
     reading output
         read 56 hmm output lines with 56 sequences in 56 events  (0 failures)
     writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
-    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
+    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
          infra time: 1.1
       hmm step time: 2.2
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
 (0.4 sec)
-      total time: 4.1
+      total time: 4.0
 cache-parameters igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 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
@@ -68,8 +68,8 @@ hmm
          infra time: 0.9
       hmm step time: 1.4
   writing hmms     removed 0  genes from glfo (leaving v 5  d 1  j 5)
-(0.4 sec)
-      total time: 2.8
+(0.3 sec)
+      total time: 2.7
 cache-parameters igl:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run 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
@@ -103,8 +103,8 @@ hmm
       hmm step time: 0.9
   writing hmms     removed 0  genes from glfo (leaving v 3  d 1  j 2)
 (0.1 sec)
-      total time: 1.6
-      total time: 12.6
+      total time: 1.7
+      total time: 12.4
 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
   warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
 partition igh:
@@ -122,22 +122,22 @@ smith-waterman
 (0.0 sec)
         water time: 0.1
 hmm
-  caching all 56 naive sequences (1.1s)
+  caching all 56 naive sequences (1.0s)
     collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
   50 clusters with 10 procs (0.6s)
    44 clusters with 7 procs (0.5s)
-   36 clusters with 5 procs (0.5s)
+   36 clusters with 5 procs (0.4s)
    31 clusters with 3 procs (0.3s)
    29 clusters with 2 procs (0.5s)
    23 clusters with 1 proc (0.6s)
    note not merging entire cpath history
-      partition loop time: 2.9
+      partition loop time: 2.8
 getting annotations for final partition
   subcluster annotating 20 clusters with steps:  (0.7s) (0.2s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
 (0.0 sec)
 
-    subcluster annotation time 0.9
+    subcluster annotation time 1.0
       total time: 5.0
 partition igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -164,7 +164,7 @@ hmm
 getting annotations for final partition
   subcluster annotating 6 clusters with steps:  (0.3s) (0.1s) (0.1s)   plotting performance (0.0 sec)
 
-    subcluster annotation time 0.4
+    subcluster annotation time 0.5
       total time: 1.5
 partition igl:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -228,7 +228,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
        joint   0.963  0.594
   merge time 0.0
   need to get annotations for 7/15 joint igh clusters
-     tag: v1.0.12
 annotate igh+igk: igh
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
@@ -246,7 +245,6 @@ hmm
     subcluster annotation time 0.6
       total time: 0.6
   need to get annotations for 13/15 joint igk clusters
-     tag: v1.0.12
 annotate igh+igk: igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igk.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
@@ -288,7 +286,6 @@ hmm
        joint   1.000  0.611
   merge time 0.0
   need to get annotations for 5/8 joint igh clusters
-     tag: v1.0.12
 annotate igh+igl: igh
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
@@ -306,7 +303,6 @@ hmm
     subcluster annotation time 0.4
       total time: 0.5
   need to get annotations for 8/8 joint igl clusters
-     tag: v1.0.12
 annotate igh+igl: igl
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igl.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
@@ -364,12 +360,9 @@ hmm
    writing merged outputs from 2 subsets to test/paired/new-results/subset-partition-new-simu/merged-subsets
     writing combined h/l info to fasta and meta files in test/paired/new-results/subset-partition-new-simu/merged-subsets
     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
-     tag: v1.0.12
-     tag: v1.0.12
-     tag: v1.0.12
 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
         log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
-      total time: 69.6
+      total time: 70.3
 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
    removing seqs very different from seed seq
                            wrong/no     removed      singly         kept   missing
@@ -407,7 +400,7 @@ getting annotations for final partition
     reading output
         read 12 hmm output lines with 17 sequences in 12 events  (0 failures)
       hmm step time: 0.3
-      total time: 1.9
+      total time: 2.0
 partition igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 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
@@ -492,7 +485,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
   merge time 0.0
      removed 7 unseeded clusters (of 8 total, leaving 1) from igh joint partition
   seed cluster size in best joint partition: 1, excluding seed seq: 0
-     tag: v1.0.12
 annotate igh+igk: igh
     removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -514,7 +506,6 @@ hmm
      removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
   need to get annotations for 1/1 joint igk clusters
   seed cluster size in best joint partition: 1, excluding seed seq: 0
-     tag: v1.0.12
 annotate igh+igk: igk
     removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -561,7 +552,7 @@ hmm
    N clusters with all seqs:
         h   12 --> 1    -11
         k    2 --> 1    -1
-      total time: 9.4
+      total time: 9.7
 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
 get-selection-metrics igh+igk: igh
 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
@@ -682,10 +673,10 @@ hmm
     skipped 1/4 clusters that had no uids in common with tree
   writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
       writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
-      total time: 5.9
+      total time: 5.8
 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
   note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
-run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/870150/meta.yaml --n-max-queries 100
+run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/929072/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
   extract_pairing_info(): read 100 sequences with 48 droplet ids
     droplet id separators (set automatically): _  indices: [0]
@@ -696,9 +687,9 @@ hmm
         2           42     0.875
         3            2     0.042
         4            2     0.042
-run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/870150 --input-metafname /tmp/runner/hmms/870150/meta.yaml --n-max-queries 100
+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
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
-  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
     read pairing info for 100 seqs from input meta file
   running vsearch on 100 sequences:
     igh:   49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -721,10 +712,10 @@ totals: igh 48 igk 37 igl 15
                2   0.13   h l
                1   0.07   h k
                1   0.07   h h k
-writing to /tmp/runner/hmms/870150/
-  igh: 48 to 870150/igh.fa
-  igk: 37 to 870150/igk.fa
-  igl: 15 to 870150/igl.fa
+writing to /tmp/runner/hmms/929072/
+  igh: 48 to 929072/igh.fa
+  igk: 37 to 929072/igk.fa
+  igl: 15 to 929072/igl.fa
 writing to paired subdirs
     igh+igk:
       igh: 36 / 48 to igh+igk/igh.fa
@@ -733,8 +724,8 @@ writing to paired subdirs
       igh: 15 / 48 to igh+igl/igh.fa
       igl: 15 / 15 to igh+igl/igl.fa
 cache-parameters igh:
-run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/870150/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/870150/meta.yaml
-  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
+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
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
 caching parameters
   vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
     keeping 23 / 198 v genes
@@ -764,8 +755,8 @@ hmm
 (1.0 sec)
       total time: 7.6
 cache-parameters igk:
-run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/870150/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/870150/meta.yaml
-  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
+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
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
 caching parameters
   vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
     keeping 16 / 64 v genes
@@ -795,8 +786,8 @@ hmm
 (1.0 sec)
       total time: 5.7
 cache-parameters igl:
-run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/870150/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/870150/meta.yaml
-  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
+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
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/929072/meta.yaml: paired-uids
 caching parameters
   vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
     keeping 10 / 80 v genes
@@ -823,7 +814,7 @@ hmm
   writing hmms     removed 0  genes from glfo (leaving v 10  d 1  j 3)
 (0.6 sec)
       total time: 3.5
-      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/870150/: failed.fa
+      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/929072/: failed.fa
       total time: 22.1
 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
 igh+igk: simulating 7 events
@@ -834,107 +825,107 @@ hmm
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-0.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.2
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-1.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 8 seqs in 0.2s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-2.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.2
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
 
       --> proc 3
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-3.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-3.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.2
+    made 1 event with 6 seqs in 0.2s (0.0s of which was running bppseqgen)
+      total time: 0.3
 
       --> proc 4
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-4.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-4.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
-      total time: 0.1
+      total time: 0.2
 
       --> proc 5
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-5.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/702692/trees-sub-5.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.2
 
       --> proc 6
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/938371/trees-sub-6.nwk
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/702692/trees-sub-6.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.2
 
    read 7 events with 40 seqs from 7 .yaml files
-      total time: 4.2
+      total time: 4.3
 simulate igh+igk: igk
 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
   note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-0.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
+    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-1.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.2
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-2.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 3
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-3.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-3.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 4
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-4.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-4.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.2
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
 
       --> proc 5
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-5.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/224927/trees-sub-5.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.2
 
       --> proc 6
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/129826/trees-sub-6.nwk
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/224927/trees-sub-6.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.1
+      total time: 0.2
 
    read 7 events with 40 seqs from 7 .yaml files
       total time: 4.1
@@ -946,21 +937,21 @@ simulating
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/373835/trees-sub-0.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/894275/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.1
+      total time: 0.2
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/373835/trees-sub-1.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/894275/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/373835/trees-sub-2.nwk
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/894275/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
@@ -973,27 +964,27 @@ simulating
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
-    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/635551/trees-sub-0.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/883242/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
-    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/635551/trees-sub-1.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/883242/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
-    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/635551/trees-sub-2.nwk
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/883242/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
    read 3 events with 13 seqs from 3 .yaml files
-      total time: 2.0
+      total time: 2.1
 igh+igk: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
 igh+igl: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
   concatenating heavy chain loci:
@@ -1006,4 +997,4 @@ simulating
   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
   removed 15 / 106 = 0.14 seqs from outfos (leaving 9 / 91 unpaired)
     writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
-      total time: 17.6
+      total time: 17.8