partis-bcr 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev7__cp312-cp312-manylinux1_x86_64.whl

test/paired/new-results/test.log

@@ -21,14 +21,14 @@ 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 0.7  processing 0.0)
+    water time: 0.7  (ig-sw 0.6  processing 0.0)
   writing hmms     removed 16 genes from glfo (leaving v 6  d 18  j 4)
 (0.5 sec)
 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 (0.5 sec)
+    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
          infra time: 1.1
       hmm step time: 2.1
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
@@ -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: 2.8
+      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
@@ -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 0.4  processing 0.0)
+    water time: 0.4  (ig-sw 0.3  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: 1.7
-      total time: 12.3
+      total time: 1.6
+      total time: 12.2
 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:
@@ -125,7 +125,7 @@ hmm
   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)
+   44 clusters with 7 procs (0.6s)
    36 clusters with 5 procs (0.4s)
    31 clusters with 3 procs (0.3s)
    29 clusters with 2 procs (0.5s)
@@ -138,7 +138,7 @@ getting annotations for final partition
 (0.0 sec)
 
     subcluster annotation time 0.9
-      total time: 4.9
+      total time: 5.0
 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 --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
@@ -331,7 +331,7 @@ hmm
         h   20 --> 23   +3
         k    6 --> 15   +9
         l    3 --> 8    +5
-      total time: 19.9
+      total time: 19.8
 subset-partition-new-simu        partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
   note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
   --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -362,7 +362,7 @@ hmm
     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
 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: 68.6
+      total time: 68.4
 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
@@ -673,10 +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: 5.6
+      total time: 5.5
 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/888813/meta.yaml --n-max-queries 100
+run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/520265/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]
@@ -687,9 +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/888813 --input-metafname /tmp/runner/hmms/888813/meta.yaml --n-max-queries 100
+run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/520265 --input-metafname /tmp/runner/hmms/520265/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/888813/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/520265/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
@@ -712,10 +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/888813/
-  igh: 48 to 888813/igh.fa
-  igk: 37 to 888813/igk.fa
-  igl: 15 to 888813/igl.fa
+writing to /tmp/runner/hmms/520265/
+  igh: 48 to 520265/igh.fa
+  igk: 37 to 520265/igk.fa
+  igl: 15 to 520265/igl.fa
 writing to paired subdirs
     igh+igk:
       igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +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/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
+run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/520265/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/520265/meta.yaml
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/520265/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
@@ -748,15 +748,15 @@ smith-waterman  (writing parameters)
 hmm
     reading output
         read 48 hmm output lines with 48 sequences in 48 events  (0 failures)
-    writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (1.9 sec)
+    writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (2.0 sec)
          infra time: 2.0
       hmm step time: 3.0
   writing hmms     removed 1  genes from glfo (leaving v 23  d 18  j 6)
-(1.0 sec)
-      total time: 7.5
+(0.9 sec)
+      total time: 7.6
 cache-parameters igk:
-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
+run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/520265/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/520265/meta.yaml
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/520265/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
@@ -783,11 +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)
-(1.1 sec)
+(1.0 sec)
       total time: 5.7
 cache-parameters igl:
-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
+run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/520265/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/520265/meta.yaml
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/520265/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
@@ -814,199 +814,187 @@ 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/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
+      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/520265/: failed.fa
+      total time: 21.8
+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
-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
+    warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
 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
+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 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --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
   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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/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)
+    made 1 event with 10 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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/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)
+    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/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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/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
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> 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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/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)
+    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/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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/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)
+    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/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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/348431/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)
+    made 1 event with 1 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
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/348431/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
+    made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.2
 
-   read 7 events with 39 seqs from 7 .yaml files
+   read 7 events with 40 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
+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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-0.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/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)
+    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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-1.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/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)
+    made 1 event with 8 seqs in 0.1s (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
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/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)
+    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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-3.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/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)
+    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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-4.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/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
+    made 1 event with 1 seqs in 0.1s (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 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-5.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/395544/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
+    made 1 event with 1 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/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
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/395544/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)
+    made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.1
 
-   read 7 events with 39 seqs from 7 .yaml files
-      total time: 4.1
+   read 7 events with 40 seqs from 7 .yaml files
+      total time: 4.0
 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
+    warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
 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
+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 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --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
   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
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/905323/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)
+    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/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
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/905323/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)
+    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 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-2.nwk
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/905323/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)
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
-   read 3 events with 27 seqs from 3 .yaml files
+   read 3 events with 13 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
+run partis simulate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igl --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1083609742 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igl.yaml
   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
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/409067/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)
+    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 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-1.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/409067/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
+    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 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-2.nwk
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/409067/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
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
 
-   read 3 events with 27 seqs from 3 .yaml files
-      total time: 2.2
+   read 3 events with 13 seqs from 3 .yaml files
+      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:
-      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)
+      h starting with 7 annotations (40 seqs)
+      k starting with 7 annotations (40 seqs)
+      h adding 3 annotations (13 seqs) for total 7 (40)
+      l starting with 3 annotations (13 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)
+     h: 10 annotations (53 seqs)
+  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: 22.8
+      total time: 17.2

test/test.py

@@ -299,8 +299,8 @@ 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_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:
@@ -936,7 +936,7 @@ 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-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')

test/trees.nwk

@@ -0,0 +1,100 @@
+((((((t5:0.0065205083289372285,t3:0.0065205083289372285):0.00022500931509783387,t7:0.006745517643935062):0.004899701229952831,(t1:0.002825027845972804,(t6:0.0017243288909834001,t10:0.0017243288909834001):0.0011006989559894037):0.008820191027915088):0.0002897695747972105,t2:0.011934988449885104):0.0007992344206923059,(t8:0.010981561979894283,(t4:0.010449007139899408,t9:0.010449007139899408):0.0005325548361948731):0.0017526608909831274):0.0007190526455930778):0.0;
+(((t1:0.0001258970141987568,t2:0.0001258970141987568):0.008179458898919231,t3:0.008305355912917988):0.005147919601949166):0.0;
+(((t7:0.009141959291085274,(t4:0.002603508111024285,t1:0.002603508111024285):0.0065384511800609885):0.00238863691202228,((((t3:0.0007869701168073406,t8:0.0007869701168073406):0.004511602509042083,t2:0.005298572626049423):0.00012755219780118975,t5:0.005426124824050613):0.002271650574021189,t6:0.007697775398071802):0.0038328208050357514):0.001922679312017934):0.0;
+((t1:0.0006977605115867409,t2:0.0006977605115867409):0.012755515003413747):0.0;
+(((t3:0.05287050335052537,(t5:0.026930500450267604,(t2:0.01960187748019478,(t4:0.013062577110129802,t6:0.013062577110129802):0.006539300371064981):0.007328622971072824):0.02594000290025776):0.04450796612044227,t1:0.09737846947096765):0.0022940356280227955):0.0;
+(((((t4:0.021655813878369522,t7:0.021655813878369522):0.00754609737143185,(t9:0.028930954397821774,(t5:0.02595504159804583,(((t10:0.0042205255246822344,t17:0.0042205255246822344):0.0113905359591424,t3:0.015611061478824635):0.009117683045313525,(t13:0.020486598618457554,t14:0.020486598618457554):0.0042421459106806066):0.0012262970749076715):0.002975912793775942):0.0002709568499795995):0.0020096117458486954,t16:0.031211522987650068):0.008580525414353968,((((t1:0.01663197558874777,(t6:0.0062756261115275045,t11:0.0062756261115275045):0.010356349479220265):0.0013316909538997363,(t15:0.0008506675798359528,t8:0.0008506675798359528):0.017112998968711553):0.0024270265108172675,t2:0.020390693058464773):0.007547202862431767,t12:0.02793789591789654):0.011854152489107496):0.0013141289639010585):0.0;
+((((t2:0.011559177998719477,t4:0.011559177998719477):0.011980991178672748,(t1:0.014158793318431492,t5:0.014158793318431492):0.009381375845960735):0.01119591956875972,t3:0.03473608873615194):0.006370088632294323):0.0;
+(t1:0.06981781729950898):0.0;
+((t2:0.03692973569052072,(t3:0.00905505912512768,t1:0.00905505912512768):0.02787467656039304):0.004176441684058889):0.0;
+((((t4:0.010579593769381347,(t5:0.0040422266327636265,(t8:0.003302800942806865,t3:0.003302800942806865):0.0007394256896567612):0.00653736713961772):0.0029673772878264794,t1:0.013546971059207826):0.01548103134909473,((t7:0.00026212476088467197,t6:0.00026212476088467197):0.01899682863888914,t2:0.01925895339887381):0.009769049018428743):0.012078174959293716):0.0;
+((t2:0.027485451520833315,t1:0.027485451520833315):0.013620725850412959):0.0;
+((t3:0.012435705410508847,((t2:0.00394371485116137,t1:0.00394371485116137):0.0009766217064399616,t4:0.004920336558201332):0.007515368853307517):0.0010175701040416373):0.0;
+(((t4:0.008232098488650112,t2:0.008232098488650112):0.020052313861583588,(t1:0.0047574693383757105,t3:0.0047574693383757105):0.02352694301185799):0.01282176502101257):0.0;
+((((t2:0.0073341960560002655,t1:0.0073341960560002655):0.0010816042810000393,t4:0.008415800337000305):0.001076595110000039,t3:0.009492395447000344):0.003960880068000143):0.0;
+((t5:0.010436162209564028,(((t7:0.0066828264947208236,(t2:0.0006264423860738302,t1:0.0006264423860738302):0.006056384108746993):0.0014022786609414195,t6:0.008085105156662243):0.0017267657019278638,(t4:0.007479007347687562,(t8:0.0011581439679516183,t3:0.0011581439679516183):0.006320863379735944):0.002332863510902544):0.0006242913508739201):0.0030171133058739595):0.0;
+((t1:0.0877159792298449,t2:0.0877159792298449):0.011956525869978857):0.0;
+(t1:0.09967250509982375):0.0;
+(((t3:0.012343791922386028,t2:0.012343791922386028):0.0009285270443794822,(t4:0.012041249512327547,t1:0.012041249512327547):0.001231069455237963):0.0001809565478349785):0.0;
+((((t1:0.0035209994550125293,t3:0.0035209994550125293):0.022044413940078444,t4:0.025565413390090976):0.014540845550051744,(t2:0.0014485310800051545,t5:0.0014485310800051545):0.03865772787013756):0.000999918425103558):0.0;
+(t1:0.04110617737124627):0.0;
+((t2:0.00910866946300033,t1:0.00910866946300033):0.004344606052000158):0.0;
+(t1:0.013453275515000487):0.0;
+(t1:0.04110617737124627):0.0;
+((t2:0.0069330800290002504,t1:0.0069330800290002504):0.006520195486000236):0.0;
+((t1:0.0017227628315122836,t2:0.0017227628315122836):0.011730512683488204):0.0;
+((((t3:0.028978127079198415,t6:0.028978127079198415):0.00029377846189187356,((t1:0.021007279289418902,t5:0.021007279289418902):0.007907223987781273,t2:0.028914503279200178):0.00035740226349011367):0.006294361375825888,t4:0.035566266919016175):0.005539910453846757):0.0;
+(t1:0.06981781729950898):0.0;
+((t2:0.07964302252985918,(t3:0.05314278384990603,t1:0.05314278384990603):0.026500238679953145):0.020029482569964584):0.0;
+(t1:0.13076504035858325):0.0;
+(((t1:0.006451360562000233,t2:0.006451360562000233):0.005218071785000189,(t3:0.006847058498000248,t4:0.006847058498000248):0.0048223738490001744):0.0017838431680000646):0.0;
+(((t8:0.009176371446472112,(t9:0.00696286069135823,t7:0.00696286069135823):0.002213510755113882):0.003890001294200135,(((t10:0.006632139421341214,(t1:0.004525366167232824,t2:0.004525366167232824):0.0021067732541083907):0.004708456193242244,t5:0.011340595610583459):0.000915067952847079,((t6:0.011628198340598254,((t11:0.0008448933648434686,t3:0.0008448933648434686):0.0025960422051335627,t12:0.0034409355701770315):0.008187262772421223):0.00012208363850628104,t4:0.011750281980604536):0.0005053815856260012):0.00081070917294171):0.00038690277541990564):0.0;
+(((t1:0.018609090978753365,t2:0.018609090978753365):0.014040303729059431,(t5:0.021133790548584233,(t3:0.01281492515914152,t4:0.01281492515914152):0.008318865389442712):0.011515604169228562):0.008456782657433473):0.0;
+(((t10:0.00903516743722709,(t13:0.002911645138073181,t6:0.002911645138073181):0.006123522299153908):0.004222491295106128,((t5:0.010906160290274114,(((t11:0.0037325677040938136,(((t16:0.0003756534651094416,t12:0.0003756534651094416):0.0012201654270306676,t9:0.0015958188920401092):0.0012036596410302527,t1:0.0027994785330703615):0.0009330891719234522):0.0053132649981335435,t15:0.009045832703227357):0.0006507630702163561,t4:0.009696595773243713):0.0012095645180304011):0.0022572010340567326,(t3:0.00821881142420657,(((t2:0.0011884612320298706,t8:0.0011884612320298706):0.0014453455820363271,t7:0.002633806814066198):0.005147528512129377,(t17:0.004634318426116479,t14:0.004634318426116479):0.003147016900079097):0.0004374760972109955):0.004944549901124275):9.429740804237007e-05):0.0001956167821049166):0.0;
+((t2:0.22281188717955536,t1:0.22281188717955536):0.2676329633754426):0.0;
+(t1:0.013453275515000487):0.0;
+(((t4:0.011509415329681546,(t2:0.00925366769474396,((t8:0.00828762393677069,(t3:0.004080500355887097,(t9:0.00033108806299083916,t6:0.00033108806299083916):0.0037494122928962573):0.004207123580883593):0.0001764281292951184,t7:0.00846405206576581):0.0007896156287781522):0.002255747637937586):0.0004944964976863178,((t5:0.008597285193762122,t11:0.008597285193762122):0.003196323681911561,(t1:0.006488893289820458,t10:0.006488893289820458):0.005304715584853224):0.00021030295499418114):0.0014493636849598976):0.0;
+((t1:0.005766500402000209,t2:0.005766500402000209):0.007686775113000278):0.0;
+((t2:0.01284740808095543,(t1:0.0020464157861521865,t3:0.0020464157861521865):0.01080099230080324):0.0006058674300450568):0.0;
+((((t11:0.03810563389023412,t4:0.03810563389023412):0.005540396806034041,t3:0.043646030700268165):0.02551521753015677,(((t8:0.00561019626003447,t6:0.00561019626003447):0.01014933119006236,t15:0.01575952745009683):0.028185081840173175,((t14:0.02939854076018063,((t2:0.011098619130068191,t13:0.011098619130068191):0.013354076220082051,((t1:0.007655101106047034,t9:0.007655101106047034):0.009067619337055712,t5:0.01672272044010275):0.0077299749120474945):0.004945845406030388):0.013892760840085361,(t7:0.03643354331022385,(t10:0.026901293420165288,t12:0.026901293420165288):0.009532249895058569):0.006857758293042136):0.000653307691804014):0.025216638930154935):0.0006565690758040341):0.0;
+(((t4:0.012213608392860183,t3:0.012213608392860183):0.00013778835573226725,(t1:0.0015043613443522913,t2:0.0015043613443522913):0.010847035402540159):0.0011018787672580378):0.0;
+(((((t1:0.004395348290097617,t4:0.004395348290097617):0.0029121170140646757,(t5:0.003507042626077888,t6:0.003507042626077888):0.003800422679084404):0.006751135586149937,t3:0.01405860089031223):0.010905203190242196,t2:0.024963804080554423):0.01614237329035851):0.0;
+(((t3:0.006422889521832168,t1:0.006422889521832168):0.022472714249412783,t2:0.028895603769244948):0.04092221352893069):0.0;
+((t6:0.008045459818427286,(((t1:0.0006928742833367977,(t5:7.757879708412012e-06,t2:7.757879708412012e-06):0.0006851164035363857):0.0015874285970843066,t3:0.002280302880121104):0.004149850828220394,t4:0.0064301537083414975):0.001615306109085787):0.005407815697287203):0.0;
+((((t6:0.009450175331085355,t4:0.009450175331085355):0.02079905348018786,(t7:0.004413011650039858,t1:0.004413011650039858):0.025836217170233353):0.0073662422170665326,(t2:0.023537724740212596,(t8:0.00946834803508552,(t3:0.004675070243042226,t5:0.004675070243042226):0.004793277791043294):0.014069376710127075):0.014077746290127152):0.0034907063380315287):0.0;
+((t2:0.15515183200897978,((t4:0.07590280129439307,t3:0.07590280129439307):0.04189864716242499,t1:0.11780144840681804):0.03735038355216174):0.008050696207465954):0.0;
+((((t5:0.029174038971651977,t6:0.029174038971651977):0.03623856360205201,(t1:0.05287038760299378,((t4:0.03586081847203062,t3:0.03586081847203062):0.015565535920881397,(t8:0.036144479482046674,t2:0.036144479482046674):0.015281874910865335):0.0014440332080817683):0.012542214970710203):0.0028487739381613114,(t7:0.0326057789518463,t9:0.0326057789518463):0.035655597562019):0.0015564407880881332):0.0;
+((t2:0.013229698420000479,t1:0.013229698420000479):0.0002235770950000081):0.0;
+(((t8:0.002615699445800805,t7:0.002615699445800805):0.010208528139222585,(((t2:0.0010149610289227073,t3:0.0010149610289227073):0.004743230394638786,t1:0.005758191423561493):0.004246415936676621,((t5:0.0019769326688494496,t4:0.0019769326688494496):0.003766309632713182,t6:0.005743242301562632):0.004261365059675482):0.002819620221785276):0.0006290479318520958):0.0;
+(((t5:0.006890384797307552,t4:0.006890384797307552):0.0006546094664292185,((t2:0.0031872455061422627,t3:0.0031872455061422627):0.0007220826458322301,(t1:0.0020747310820926055,t6:0.0020747310820926055):0.0018345970690818872):0.003635666112162278):0.005908281251263716):0.0;
+((t4:0.013142541629853942,((t2:0.0003208099471964347,t1:0.0003208099471964347):0.004570934548949202,t3:0.004891744495945635):0.008250797134908306):0.00031073388429654663):0.0;
+(t1:0.09967250509982375):0.0;
+(t1:0.04110617737124627):0.0;
+(((t13:0.0612299056807233,((t7:0.03861328947045613,(t9:0.03780974739044664,((t14:0.01551212498018324,t16:0.01551212498018324):0.0196313167102319,(t3:0.006583683447077772,(t8:0.0005242477475061928,t5:0.0005242477475061928):0.006059435700071579):0.02855975824033737):0.0026663057020314966):0.0008035420790094921):0.015761554540186188,(t11:0.048153063420568826,(t1:0.0302808943303577,((t18:0.014165036910167328,t12:0.014165036910167328):0.008451443368099835,t19:0.022616480280267165):0.007664414056090538):0.01787216909021112):0.006221780596073497):0.006855061669080977):0.0057081495020674285,(((t4:0.008645301197102126,t10:0.008645301197102126):0.023117663960273083,t15:0.0317629651603752):0.03424191082040449,((t2:0.024166396460285473,t6:0.024166396460285473):0.01959496464023147,t17:0.04376136111051694):0.02224351487026276):0.0009331792070110234):0.002879762115034018):0.0;
+(t1:0.13076504035858325):0.0;
+(((t3:0.013208836408472462,(t2:0.006323124391268761,t4:0.006323124391268761):0.0068857120142037):0.012033246058608414,t1:0.025242082457080876):0.015864094908165396):0.0;
+(((t1:0.022212139128151755,t2:0.022212139128151755):0.01693750110859065,t3:0.0391496402267424):0.0019565371378371986):0.0;
+(t1:0.04110617737124627):0.0;
+(t1:0.04110617737124627):0.0;
+(((((((((t8:0.005718735848822636,t20:0.005718735848822636):0.0002813924915912728,t12:0.00600012834081391):0.0010009312339689567,(t21:0.002005163522937811,t22:0.002005163522937811):0.004995896050845055):0.0044449012868621445,t14:0.01144596085964501):0.00034364485038934205,(t6:0.010164251789684761,((t5:0.0019062012219408801,t7:0.0019062012219408801):0.003283657352898159,(t1:0.004382334625864084,(t9:0.003194448534900926,t11:0.003194448534900926):0.0011878860909631584):0.0008075239490749551):0.0049743932148457225):0.0016253539229495906):0.0007078678900780459,(t10:0.012216333809621118,(t16:0.010262027359681729,((t4:0.002961978410908136,t18:0.002961978410908136):0.004913297285847617,t19:0.007875275696755753):0.002386751659925976):0.0019543064519393885):0.0002811397932912806):3.3240558168969066e-05,(t3:0.005803328292820013,t15:0.005803328292820013):0.006727385867791354):0.0004542689972859111,((t2:0.0021383244999336813,t17:0.0021383244999336813):0.008446042123738052,t13:0.010584366619671732):0.002400616533925546):0.0004682923574854762):0.0;
+(((t3:0.01258314914029987,t1:0.01258314914029987):0.00031536683040751557,t2:0.012898515970307386):0.028207661400672223):0.0;
+((((t12:0.029856472439910613,(t10:0.029629187069911293,(t15:0.02261888475993228,((t8:0.004852251667985473,t1:0.004852251667985473):0.010840176649967545,t14:0.015692428319953017):0.006926456433979262):0.007010302308979011):0.00022728537419931954):0.007134532015978639,(t2:0.0331993323899006,(t9:0.025834153599922655,((((t13:0.010249100449969314,t5:0.010249100449969314):0.003480118823989581,t3:0.013729219279958895):0.0068936983049793605,t7:0.020622917579938258):6.804153550979629e-05,t6:0.020690959119938054):0.005143194479984602):0.007365178791977949):0.003791672065988648):0.003351523083989966,(t4:0.012112889039963735,t11:0.012112889039963735):0.028229638499915482):0.0007636498318977136):0.0;
+(t1:0.013453275515000487):0.0;
+(((t2:0.0011786652770930824,t3:0.0011786652770930824):0.019658714911552504,t1:0.020837380191645587):0.020268797181600684):0.0;
+((t3:0.05846602929960331,((t1:0.008705722570940932,t2:0.008705722570940932):0.022354910759848322,t4:0.031060633329789256):0.027405395969814058):0.04120647579972042):0.0;
+((t3:0.011385421789436216,(t2:0.0070952932206486555,t1:0.0070952932206486555):0.004290128569787562):0.002067853724897604):0.0;
+((((t3:0.0006326856984254547,t1:0.0006326856984254547):0.010344396960416186,t2:0.01097708265044164):0.04863971803195692,t4:0.05961680069239856):0.010201016610410417):0.0;
+(t1:0.013453275515000487):0.0;
+((t2:0.005734956699000207,t1:0.005734956699000207):0.0077183188160002796):0.0;
+((((t12:0.03064615586705234,(t6:0.008642768979168707,t2:0.008642768979168707):0.022003386887883634):0.0023316529507757333,((t11:0.003237068437688647,t5:0.003237068437688647):0.028756253997234117,t1:0.031993322436922766):0.0009844863817053085):0.004258147912590436,(((t3:0.010785851158962578,t9:0.010785851158962578):0.013066849088743183,(t8:0.02083112862799639,(t10:0.011154049078927164,t7:0.011154049078927164):0.009677079542069224):0.0030215716167093743):0.003130714972698877,t4:0.02698341521740464):0.010252541519013874):0.003870220638627748):0.0;
+((t1:0.03212197728019244,t2:0.03212197728019244):0.008984200091053825):0.0;
+(t1:0.013453275515000487):0.0;
+((((t3:0.010774106778688503,t4:0.010774106778688503):0.00970156362881906,t2:0.02047567040750756):0.0060809161442597895,t1:0.02655658655676735):0.014549590818228923):0.0;
+(((t3:0.008367011731000304,t2:0.008367011731000304):0.004029842149000146,t1:0.012396853880000449):0.001056421635000038):0.0;
+(((t1:0.005736453449858075,t2:0.005736453449858075):0.00039748736249016584,t3:0.0061339408118482415):0.007319334702818914):0.0;
+(t1:0.013453275515000487):0.0;
+((t1:0.003640462452000132,t2:0.003640462452000132):0.009812813063000355):0.0;
+(t1:0.013453275515000487):0.0;
+(t1:0.04110617737124627):0.0;
+(t1:0.013453275515000487):0.0;
+((t3:0.0960190268829611,(t1:0.09264831400285714,(t4:0.0830742404425619,t2:0.0830742404425619):0.009574073562295251):0.003370712877103948):0.0036534782181126685):0.0;
+(((((t4:0.022397323160180973,t2:0.022397323160180973):0.07639099786061726,t5:0.09878832101079824):0.011909985760096236,t3:0.11069830680089446):0.10255413240082865,t1:0.21325243920172313):0.01936375704015646):0.0;
+(((t6:0.0307069075821262,((t2:0.00954409627366085,t1:0.00954409627366085):0.0188932213413082,(t3:0.00473659063732797,t4:0.00473659063732797):0.02370072697164108):0.00226958997015715):0.010045605940695576,t5:0.040752513522821776):0.00035366384842448826):0.0;
+(((((t7:0.013015670059271229,t1:0.013015670059271229):0.00724499697959434,t11:0.02026066703886557):0.023334953498693432,(t5:0.04188215155765494,t3:0.04188215155765494):0.00171346898090406):0.023786086608668176,((t10:0.008298309023535363,t6:0.008298309023535363):0.05457985917694398,((t4:0.02490817720860535,(t2:0.00010602953329406322,t8:0.00010602953329406322):0.024802147668611284):0.016494287159076453,t9:0.04140246436768181):0.021475703838797537):0.004503538940747839):0.0024361101548635977):0.0;
+(t1:0.013453275515000487):0.0;
+(((t11:0.011075661090178986,((t9:0.00024410677040394486,t10:0.00024410677040394486):0.005457233939088191,((t1:0.003265183452052767,t3:0.003265183452052767):0.0017931747180289783,(t4:0.004379598497070776,((t12:0.00024134001020390013,t13:0.00024134001020390013):9.288899454150112e-05,t8:0.0003342290047054013):0.004045369493065375):0.000678759672510969):0.0006429825396103909):0.0053743203810868515):0.0017771038500287188,((t6:0.008409141961135895,t5:0.008409141961135895):0.003538033666057176,(t2:0.00012760397410206212,t7:0.00012760397410206212):0.011819571650191008):0.0009055893139146347):0.0006005105746097045):0.0;
+(((((t1:0.0024675422970505292,t5:0.0024675422970505292):0.002044109531041858,t4:0.004511651828092387):0.0032930244110674326,t8:0.0078046762391598195):0.004358697702089255,((t3:0.003796717250077747,t7:0.003796717250077747):0.0007990872145163632,(t2:0.003713534178076043,t6:0.003713534178076043):0.0008822702864180666):0.007567569476154964):0.0012899015740264138):0.0;
+(t1:0.06981781729950898):0.0;
+(((t3:0.006225125161956265,((t1:0.0021976056619845605,t6:0.0021976056619845605):0.00393852634197233,((t8:0.0011919082389916262,t9:0.0011919082389916262):0.0006340812053955452,t7:0.0018259894439871715):0.004310142559969719):8.899315704937479e-05):0.003031972547978699,(t10:0.00542439613696189,((t2:0.0010541334419925943,t4:0.0010541334419925943):0.004037375788971636,t5:0.00509150923196423):0.00033288690529766134):0.003832701571973073):0.00419617780597052):0.0;
+(((t1:0.006949864029586977,(t4:0.004732833068718733,t3:0.004732833068718733):0.0022170309618682444):0.0052880160376857395,(t2:0.0012352686989265892,t5:0.0012352686989265892):0.011002611369346127):0.0012153954469277704):0.0;
+(t1:0.013453275515000487):0.0;
+((t1:0.020038044869859075,t2:0.020038044869859075):0.049779772429649906):0.0;
+(t1:0.06981781729950898):0.0;
+(t1:0.04110617737124627):0.0;
+((t1:0.03486468296071778,(t2:0.03156602991064987,((t5:0.01701226546035024,t3:0.01701226546035024):0.006053445144124625,t4:0.023065710610474868):0.008500319300175):0.003298653051067911):0.006241494412128497):0.0;
+((t5:0.012756817909810817,(t4:0.010426073709845381,(t2:0.009232871403863077,(t1:0.006254425543907247,t3:0.006254425543907247):0.0029784458599558298):0.0011932023069823048):0.0023307441969654353):0.0006964576069896716):0.0;
+(((t2:0.0048118160290001755,t3:0.0048118160290001755):0.005959868198000217,(t1:0.010543766840000383,(t4:0.007625172533000278,t5:0.007625172533000278):0.0029185943040001064):0.0002279173890000083):0.0026815912880000974):0.0;
+((t1:0.03758287626862516,(t3:0.03199778352882946,(t2:0.014615515219465339,t4:0.014615515219465339):0.017382268309364127):0.005585092736795688):0.0035233011048711113):0.0;
+(t1:0.013453275515000487):0.0;
+((t2:0.009748924202000355,t1:0.009748924202000355):0.0037043513130001347):0.0;
+((t1:0.14040191872346797,(t3:0.12859899072149514,t2:0.12859899072149514):0.011802927921972841):0.02280060953381109):0.0;