partis-bcr 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

test/paired/new-results/test.log

@@ -21,7 +21,7 @@ smith-waterman  (writing parameters)
       kept 25 (0.446) unproductive
         writing sw results to test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
     writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
-    water time: 0.7  (ig-sw 0.6  processing 0.0)
+    water time: 0.7  (ig-sw 0.7  processing 0.0)
   writing hmms     removed 16 genes from glfo (leaving v 6  d 18  j 4)
 (0.5 sec)
 hmm
@@ -30,10 +30,10 @@ hmm
     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 (0.5 sec)
          infra time: 1.1
-      hmm step time: 2.2
+      hmm step time: 2.1
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
-(0.4 sec)
-      total time: 4.0
+(0.3 sec)
+      total time: 3.9
 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
@@ -69,7 +69,7 @@ hmm
       hmm step time: 1.4
   writing hmms     removed 0  genes from glfo (leaving v 5  d 1  j 5)
 (0.4 sec)
-      total time: 2.7
+      total time: 2.8
 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
@@ -91,7 +91,7 @@ smith-waterman  (writing parameters)
       kept 14 (0.667) unproductive
         writing sw results to test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
     writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.3 sec)
-    water time: 0.4  (ig-sw 0.3  processing 0.0)
+    water time: 0.4  (ig-sw 0.4  processing 0.0)
   writing hmms     removed 7  genes from glfo (leaving v 3  d 1  j 2)
 (0.1 sec)
 hmm
@@ -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: 12.2
+      total time: 1.7
+      total time: 12.3
 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:
@@ -122,7 +122,7 @@ 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 (0.5s)
    44 clusters with 7 procs (0.5s)
@@ -137,8 +137,8 @@ getting annotations for final partition
     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 1.0
-      total time: 5.0
+    subcluster annotation time 0.9
+      total time: 4.9
 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 --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
 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 0.5
+    subcluster annotation time 0.4
       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: v1.0.11
 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: v1.0.11
 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
@@ -262,7 +260,7 @@ smith-waterman
 hmm
   subcluster annotating 15 clusters with steps:  (0.3s) (0.1s) 
     subcluster annotation time 0.4
-      total time: 0.4
+      total time: 0.5
 igh+igl: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 7 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 3  l 4
             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
@@ -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: v1.0.11
 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: v1.0.11
 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: v1.0.11
-     tag: v1.0.11
-     tag: v1.0.11
 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: 68.2
+      total time: 68.6
 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
@@ -430,7 +423,7 @@ hmm
 getting annotations for final partition
   subcluster annotating 2 clusters with steps:  (0.1s) (0.1s) (0.1s) 
     subcluster annotation time 0.2
-      total time: 0.7
+      total time: 0.6
 partition igl:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 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
@@ -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: v1.0.11
 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: v1.0.11
 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)
@@ -685,7 +676,7 @@ hmm
       total time: 5.6
 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/275115/meta.yaml --n-max-queries 100
+run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/888813/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/275115 --input-metafname /tmp/runner/hmms/275115/meta.yaml --n-max-queries 100
+run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/888813 --input-metafname /tmp/runner/hmms/888813/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/275115/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/888813/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/275115/
-  igh: 48 to 275115/igh.fa
-  igk: 37 to 275115/igk.fa
-  igl: 15 to 275115/igl.fa
+writing to /tmp/runner/hmms/888813/
+  igh: 48 to 888813/igh.fa
+  igk: 37 to 888813/igk.fa
+  igl: 15 to 888813/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/275115/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/275115/meta.yaml
-  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
+run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/888813/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/888813/meta.yaml
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/888813/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: 7.5
 cache-parameters igk:
-run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
-  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
+run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/888813/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/888813/meta.yaml
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/888813/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
@@ -792,11 +783,11 @@ hmm
          infra time: 1.3
       hmm step time: 1.9
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
-(1.0 sec)
+(1.1 sec)
       total time: 5.7
 cache-parameters igl:
-run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/275115/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/275115/meta.yaml
-  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/275115/meta.yaml: paired-uids
+run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/888813/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/888813/meta.yaml
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/888813/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
@@ -823,5 +814,199 @@ 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/275115/: failed.fa
-      total time: 21.8
+      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/888813/: 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 --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
+generate-trees igh+igk: igh
+run partis simulate --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-trees 7 --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 --no-per-base-mutation --random-seed 2003260051 --indel-frequency 0.2 --generate-trees --outfname test/paired/new-results/test/simu/igh+igk/trees.nwk
+  note: reducing --n-procs to 1 (was 4) so it isn't bigger than --n-sim-events
+  generating 7 trees, n-leaves from geometric distribution with parameter 5.0
+    mean over 7 trees:   depth 0.02051   leaves 5.57
+    writing trees to test/paired/new-results/test/simu/igh+igk/trees.nwk
+      total time: 1.3
+simulate igh+igk: igh
+run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --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 --no-per-base-mutation --random-seed 2003260051 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igh.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igk/trees.nwk
+  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/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 12 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.1
+
+      --> 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 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.2s (0.0s of which was running bppseqgen)
+      total time: 0.2
+
+      --> 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 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 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 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-3.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 2 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/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-4.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 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 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-5.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.1
+
+      --> 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 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-6.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: 0.1
+
+   read 7 events with 39 seqs from 7 .yaml files
+      total time: 4.1
+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 --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 --input-simulation-treefname test/paired/new-results/test/simu/igh+igk/trees.nwk
+  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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 12 seqs in 0.1s (0.1s 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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 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/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-2.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-3.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 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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-4.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: 0.0
+
+      --> 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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-5.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 9 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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-6.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: 0.1
+
+   read 7 events with 39 seqs from 7 .yaml files
+      total time: 4.1
+igh+igl: simulating 3 events
+generate-trees igh+igl: igh
+run partis simulate --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-trees 3 --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 --no-per-base-mutation --random-seed 982264879 --indel-frequency 0.2 --generate-trees --outfname test/paired/new-results/test/simu/igh+igl/trees.nwk
+  note: reducing --n-procs to 1 (was 4) so it isn't bigger than --n-sim-events
+  generating 3 trees, n-leaves from geometric distribution with parameter 5.0
+    mean over 3 trees:   depth 0.05242   leaves 9.00
+    writing trees to test/paired/new-results/test/simu/igh+igl/trees.nwk
+      total time: 1.3
+simulate igh+igl: igh
+run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --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 --no-per-base-mutation --random-seed 982264879 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igh.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igl/trees.nwk
+  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
+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 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 14 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/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 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 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-2.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
+
+   read 3 events with 27 seqs from 3 .yaml files
+      total time: 2.0
+simulate igh+igl: igl
+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 --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 --input-simulation-treefname test/paired/new-results/test/simu/igh+igl/trees.nwk
+  note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
+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 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-0.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 14 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/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
+    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-1.nwk
+      using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
+    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.0
+
+      --> 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 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-2.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: 0.0
+
+   read 3 events with 27 seqs from 3 .yaml files
+      total time: 2.2
+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:
+      h starting with 7 annotations (39 seqs)
+      k starting with 7 annotations (39 seqs)
+      h adding 3 annotations (27 seqs) for total 7 (39)
+      l starting with 3 annotations (27 seqs)
+    finished with:
+     h: 10 annotations (66 seqs)
+  apportioned 132 seqs among 52 droplets (mean/2 1.3): 4 2 2 2 2 4 2 2 2 2 2 2 4 2 2 2 4 4 2 2 4 2 2 2 2 2 2 4 2 2 4 2 4 2 2 2 2 2 2 2 2 2 4 4 2 4 2 2 2 4 4 2
+  removed 19 / 132 = 0.14 seqs from outfos (leaving 7 / 113 unpaired)
+    writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
+      total time: 22.8

test/test.py

@@ -299,6 +299,10 @@ class Tester(object):
 
         if ptest == 'simulate':
             argfo['parameter-dir'] = self.paramdir(input_stype, 'data')
+            # if args.no_tree_gen:
+            #     argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
+            if args.no_per_base_mutation:
+                argfo['extras'] += ['--no-per-base-mutation']
         else:
             argfo['inpath'] = self.inpath('new' if args.bust_cache else 'ref', input_dtype)
             if ptest.find('subset-') != 0:
@@ -932,6 +936,8 @@ parser.add_argument('--only-bust-current', action='store_true', help='only bust
 parser.add_argument('--paired', action='store_true', help='run paired tests, i.e. with --paired-loci. Note that this doesn\'t test all the things (e.g. seed partitioning) that non-paired does.')
 parser.add_argument('--run-all', action='store_true', help='run all four combinations of tests: paired/non-paired and slow/non-slow (by default only runs one). *Not* for use with --bust-cache, which runs all of them by default.')
 parser.add_argument('--no-simu', action='store_true', help='don\'t run simulation, e.g. if using a minimal install')
+# parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
+parser.add_argument('--no-per-base-mutation', action='store_true', help='use simpler, non-per-base mutation model (to avoid bpp-newlik compilation)')
 parser.add_argument('--ig-or-tr', default='ig')
 parser.add_argument('--print-width', type=int, default=300, help='set to 0 for infinite')