partis-bcr 1.0.13.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl

test/paired/new-results/test.log

@@ -5,7 +5,7 @@
 run partis cache-parameters --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
   --input-metafnames: added meta info for 56 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
 caching parameters
-  vsearch: 56 / 56 v annotations (0 failed) with 9 v genes in 0.2 sec
+  vsearch: 56 / 56 v annotations (0 failed) with 9 v genes in 0.1 sec
     keeping 6 / 198 v genes
     missing 17 simulation genes (counts): hv1-1801 0  hv1-4603 0  hv1-801 0  hv2-502 0  hv3-1101 0  hv3-1501 0  hv3-2001 0  hv3-2101 0  hv3-2301 0  hv3-3004 0  hv3-4802 0  hv3-6601 0  hv3-7401 0  hv3-901 0  hv4-3103 0  hv4-402 0  hv4-5911 0
 smith-waterman  (new-allele fitting)
@@ -13,31 +13,31 @@ smith-waterman  (new-allele fitting)
     running 10 procs for 56 seqs
       info for 56 / 56 = 1.000   (removed: 0 failed)
       kept 25 (0.446) unproductive
-    water time: 0.2  (ig-sw 0.1  processing 0.1)
+    water time: 0.2  (ig-sw 0.1  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.2 sec
+  vsearch: 56 / 56 v annotations (0 failed) with 6 v genes in 0.1 sec
     running 10 procs for 56 seqs
       info for 56 / 56 = 1.000   (removed: 0 failed)
       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 (0.8 sec)
-    water time: 1.1  (ig-sw 0.9  processing 0.1)
+    writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (1.1 sec)
+    water time: 1.5  (ig-sw 1.3  processing 0.2)
   writing hmms     removed 16 genes from glfo (leaving v 6  d 18  j 4)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.7 sec)
+(0.9 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 (0.8 sec)
-    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.7 sec)
-         infra time: 1.7
-      hmm step time: 2.5
+    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.8 sec)
+         infra time: 1.8
+      hmm step time: 3.2
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.7 sec)
-      total time: 5.7
+(0.8 sec)
+      total time: 7.1
 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
@@ -52,7 +52,7 @@ smith-waterman  (new-allele fitting)
     running 11 procs for 2 seqs
       info for 36 / 36 = 1.000   (removed: 0 failed)
       kept 14 (0.389) unproductive
-    water time: 0.3  (ig-sw 0.0  processing 0.1)
+    water time: 0.4  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
   vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
     running 10 procs for 36 seqs
@@ -60,24 +60,24 @@ smith-waterman  (writing parameters)
       info for 36 / 36 = 1.000   (removed: 0 failed)
       kept 14 (0.389) unproductive
         writing sw results to test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
-    writing parameters to test/paired/new-results/test/parameters/simu/igk/sw (0.6 sec)
-    water time: 1.0  (ig-sw 0.7  processing 0.1)
+    writing parameters to test/paired/new-results/test/parameters/simu/igk/sw (0.8 sec)
+    water time: 1.2  (ig-sw 0.8  processing 0.1)
   writing hmms     removed 2  genes from glfo (leaving v 5  d 1  j 5)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.4 sec)
+(0.5 sec)
 hmm
     reading output
         read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
-    writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.6 sec)
-    writing parameters to test/paired/new-results/test/parameters/simu/igk/true (0.7 sec)
-         infra time: 1.4
-      hmm step time: 1.8
+    writing parameters to test/paired/new-results/test/parameters/simu/igk/hmm (0.8 sec)
+    writing parameters to test/paired/new-results/test/parameters/simu/igk/true (0.6 sec)
+         infra time: 1.6
+      hmm step time: 2.2
   writing hmms     removed 0  genes from glfo (leaving v 5  d 1  j 5)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.5 sec)
-      total time: 4.4
+(0.6 sec)
+      total time: 5.3
 cache-parameters igl:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis cache-parameters --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -103,20 +103,20 @@ smith-waterman  (writing parameters)
   writing hmms     removed 7  genes from glfo (leaving v 3  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.3 sec)
+(0.4 sec)
 hmm
     reading output
         read 21 hmm output lines with 21 sequences in 21 events  (0 failures)
     writing parameters to test/paired/new-results/test/parameters/simu/igl/hmm (0.4 sec)
     writing parameters to test/paired/new-results/test/parameters/simu/igl/true (0.4 sec)
-         infra time: 1.0
-      hmm step time: 1.4
+         infra time: 0.9
+      hmm step time: 1.3
   writing hmms     removed 0  genes from glfo (leaving v 3  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.2 sec)
-      total time: 3.1
-      total time: 18.9
+(0.3 sec)
+      total time: 3.4
+      total time: 22.6
 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:
@@ -132,25 +132,25 @@ smith-waterman
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
 (0.0 sec)
-        water time: 0.1
+        water time: 0.2
 hmm
-  caching all 56 naive sequences (1.2s)
+  caching all 56 naive sequences (2.2s)
     collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
-  50 clusters with 10 procs (0.8s)
-   44 clusters with 7 procs (0.8s)
+  50 clusters with 10 procs (1.0s)
+   44 clusters with 7 procs (0.9s)
    36 clusters with 5 procs (0.7s)
-   31 clusters with 3 procs (0.5s)
+   31 clusters with 3 procs (0.6s)
    29 clusters with 2 procs (0.9s)
-   23 clusters with 1 proc (1.1s)
+   23 clusters with 1 proc (1.0s)
    note not merging entire cpath history
-      partition loop time: 4.7
+      partition loop time: 4.9
 getting annotations for final partition
-  subcluster annotating 20 clusters with steps:  (0.8s) (0.3s)   plotting performance 
+  subcluster annotating 20 clusters with steps:  (0.9s) (0.3s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
 (0.0 sec)
 
-    subcluster annotation time 1.2
-      total time: 7.5
+    subcluster annotation time 1.3
+      total time: 8.9
 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
@@ -164,27 +164,27 @@ smith-waterman
   plotting performance (0.0 sec)
         water time: 0.1
 hmm
-  caching all 36 naive sequences (0.5s)
+  caching all 36 naive sequences (0.6s)
     collapsed 36 queries into 7 clusters with identical naive seqs (0.0 sec)
   reducing n procs to number of clusters: 10 --> 7
   7 clusters with 7 procs (0.3s)
-   7 clusters with 5 procs (0.3s)
+   7 clusters with 5 procs (0.2s)
    7 clusters with 3 procs (0.3s)
    7 clusters with 2 procs (0.3s)
-   6 clusters with 1 proc (0.4s)
+   6 clusters with 1 proc (0.5s)
        partition loop time: 1.5
 getting annotations for final partition
-  subcluster annotating 6 clusters with steps:  (0.4s) (0.2s) (0.2s)   plotting performance (0.0 sec)
+  subcluster annotating 6 clusters with steps:  (0.6s) (0.2s) (0.2s)   plotting performance (0.0 sec)
 
-    subcluster annotation time 0.9
-      total time: 3.2
+    subcluster annotation time 1.0
+      total time: 3.4
 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 --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igl --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
   --input-metafnames: added meta info for 21 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
 partitioning     (with test/paired/new-results/test/parameters/simu/igl/hmm)
 smith-waterman
-  vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.1 sec
+  vsearch: 21 / 21 v annotations (0 failed) with 3 v genes in 0.2 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
       info for 21 / 21 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 14 (0.667) unproductive
@@ -195,14 +195,14 @@ hmm
     collapsed 21 queries into 3 clusters with identical naive seqs (0.0 sec)
   reducing n procs to number of clusters: 10 --> 3
   3 clusters with 3 procs (0.2s)
-   3 clusters with 2 procs (0.1s)
-   3 clusters with 1 proc (0.2s)
+   3 clusters with 2 procs (0.2s)
+   3 clusters with 1 proc (0.3s)
        partition loop time: 0.6
 getting annotations for final partition
-  subcluster annotating 3 clusters with steps:  (0.3s) (0.2s) (0.2s)   plotting performance (0.0 sec)
+  subcluster annotating 3 clusters with steps:  (0.4s) (0.3s) (0.2s)   plotting performance (0.0 sec)
 
-    subcluster annotation time 0.7
-      total time: 2.0
+    subcluster annotation time 0.9
+      total time: 2.2
 combining chains
 cleaning pair info for 113 seqs
      synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0  k 0  l 0
@@ -247,15 +247,15 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
   --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
 annotating    (with test/paired/new-results/test/parameters/simu/igh/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.6 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 13 (0.361) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 15 clusters with steps:  (0.7s) (0.2s) 
-    subcluster annotation time 0.9
-      total time: 1.0
+  subcluster annotating 15 clusters with steps:  (1.2s) (0.2s) 
+    subcluster annotation time 1.5
+      total time: 2.2
   need to get annotations for 13/15 joint igk clusters
 annotate igh+igk: igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -264,14 +264,14 @@ hmm
   --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
 annotating    (with test/paired/new-results/test/parameters/simu/igk/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.2 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 5 v genes in 0.1 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 14 (0.389) unproductive
-        water time: 0.0
+        water time: 0.1
 hmm
-  subcluster annotating 15 clusters with steps:  (0.5s) (0.2s) 
-    subcluster annotation time 0.7
+  subcluster annotating 15 clusters with steps:  (0.6s) (0.2s) 
+    subcluster annotation time 0.8
       total time: 1.0
 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
@@ -305,15 +305,15 @@ hmm
   --input-partition-fname: read best partition with 20 sequences in 8 clusters from test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
 annotating    (with test/paired/new-results/test/parameters/simu/igh/hmm)
 smith-waterman
-  vsearch: 20 / 20 v annotations (0 failed) with 4 v genes in 0.2 sec
+  vsearch: 20 / 20 v annotations (0 failed) with 4 v genes in 0.1 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
       info for 20 / 20 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 12 (0.600) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 8 clusters with steps:  (0.4s) (0.3s) 
+  subcluster annotating 8 clusters with steps:  (0.5s) (0.3s) 
     subcluster annotation time 0.7
-      total time: 0.9
+      total time: 0.8
   need to get annotations for 8/8 joint igl clusters
 annotate igh+igl: igl
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -328,9 +328,9 @@ smith-waterman
       kept 14 (0.667) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 8 clusters with steps:  (0.3s) (0.1s) 
-    subcluster annotation time 0.5
-      total time: 0.6
+  subcluster annotating 8 clusters with steps:  (0.4s) (0.2s) 
+    subcluster annotation time 0.6
+      total time: 0.7
   concatenating heavy chain loci:
       h starting with 15 annotations (36 seqs)
       k starting with 15 annotations (36 seqs)
@@ -343,7 +343,7 @@ hmm
         h   20 --> 23   +3
         k    6 --> 15   +9
         l    3 --> 8    +5
-      total time: 33.5
+      total time: 39.8
 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
@@ -374,7 +374,7 @@ 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: 115.5
+      total time: 155.3
 seed-partition-new-simu          partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
    removing seqs very different from seed seq
                            wrong/no     removed      singly         kept   missing
@@ -393,26 +393,26 @@ hmm
   --input-metafnames: added meta info for 17 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
 partitioning     (with test/paired/new-results/test/parameters/simu/igh/hmm)
 smith-waterman
-  vsearch: 17 / 17 v annotations (0 failed) with 3 v genes in 0.2 sec
+  vsearch: 17 / 17 v annotations (0 failed) with 3 v genes in 0.1 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml
       info for 17 / 17 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 8 (0.471) unproductive
         water time: 0.0
 hmm
-  caching all 17 naive sequences (0.5s)
+  caching all 17 naive sequences (0.7s)
     collapsed 17 queries into 17 clusters with identical naive seqs (0.0 sec)
   17 clusters with 10 procs (0.4s)
    17 clusters with 7 procs (0.4s)
    17 clusters with 5 procs (0.4s)
-   17 clusters with 3 procs (0.4s)
+   17 clusters with 3 procs (0.5s)
    14 clusters with 2 procs (0.4s)
-   14 clusters with 1 proc (0.5s)
-       partition loop time: 2.5
+   14 clusters with 1 proc (0.6s)
+       partition loop time: 2.6
 getting annotations for final partition
     reading output
         read 12 hmm output lines with 17 sequences in 12 events  (0 failures)
       hmm step time: 0.4
-      total time: 3.6
+      total time: 3.9
 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 --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igk.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -430,12 +430,12 @@ hmm
   reducing n procs to number of clusters: 10 --> 3
   3 clusters with 3 procs (0.2s)
    3 clusters with 2 procs (0.2s)
-   3 clusters with 1 proc (0.2s)
-       partition loop time: 0.5
+   3 clusters with 1 proc (0.3s)
+       partition loop time: 0.7
 getting annotations for final partition
-  subcluster annotating 2 clusters with steps:  (0.2s) (0.2s) (0.2s) 
+  subcluster annotating 2 clusters with steps:  (0.3s) (0.2s) (0.2s) 
     subcluster annotation time 0.6
-      total time: 1.6
+      total time: 1.7
 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
@@ -443,7 +443,7 @@ getting annotations for final partition
   note: reducing N procs to the number of seqs 10 --> 4
 partitioning     (with test/paired/new-results/test/parameters/simu/igl/hmm)
 smith-waterman
-  vsearch: 4 / 4 v annotations (0 failed) with 2 v genes in 0.1 sec
+  vsearch: 4 / 4 v annotations (0 failed) with 2 v genes in 0.2 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
       info for 4 / 4 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
         water time: 0.0
@@ -457,8 +457,8 @@ hmm
 getting annotations for final partition
     reading output
         read 2 hmm output lines with 4 sequences in 2 events  (0 failures)
-      hmm step time: 0.1
-      total time: 0.9
+      hmm step time: 0.2
+      total time: 1.1
 combining chains
 cleaning pair info for 33 seqs
      synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0  k 0  l 0
@@ -527,7 +527,7 @@ hmm
   --input-partition-fname: read best partition with 1 sequences in 1 clusters from test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/igh+igk/partition-igk-only-partition.yaml
 annotating    (with test/paired/new-results/test/parameters/simu/igk/hmm)
 smith-waterman
-  vsearch: 1 / 1 v annotations (0 failed) with 1 v gene in 0.1 sec
+  vsearch: 1 / 1 v annotations (0 failed) with 1 v gene in 0.2 sec
         reading sw results from test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml
       info for 1 / 1 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 1 (1.000) unproductive
@@ -535,8 +535,8 @@ smith-waterman
 hmm
     reading output
         read 1 hmm output lines with 1 sequences in 1 events  (0 failures)
-      hmm step time: 0.1
-      total time: 0.2
+      hmm step time: 0.2
+      total time: 0.4
 igh+igl: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 1 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 1  l 0
             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
@@ -564,7 +564,7 @@ hmm
    N clusters with all seqs:
         h   12 --> 1    -11
         k    2 --> 1    -1
-      total time: 15.9
+      total time: 23.7
 get-selection-metrics-new-simu   partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
 get-selection-metrics igh+igk: igh
 run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -600,7 +600,7 @@ hmm
       starting 2 jobs
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/input-seqs.fa
-      made 2 fasttree trees (0.2s)
+      made 2 fasttree trees (0.3s)
     tree origins: 2 ran fasttree
     skipped 2/4 clusters smaller than 4
       setting default tau to 1 / 337 = 0.0030
@@ -611,7 +611,7 @@ hmm
       warning get_aa_tree() (AA inf tree, iclust 1): skipped 2/9 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: eov
     skipped 2/4 clusters that had no uids in common with tree
   writing selection metrics to test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml
-      total time: 0.3
+      total time: 0.4
 get-selection-metrics igh+igl: igh
 run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml
   note: --parameter-dir not set, so using default: x-dummy-x
@@ -632,7 +632,7 @@ hmm
     calculating normalized lb index and lb ratio and lb fraction on aa tree with tau 0.0027
     skipped 1/2 clusters that had no uids in common with tree
   writing selection metrics to test/paired/new-results/partition-new-simu/igh+igl/partition-igh-selection-metrics.yaml
-      total time: 0.2
+      total time: 0.3
 get-selection-metrics igh+igl: igl
 run partis get-selection-metrics --locus igl --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml
   note: --parameter-dir not set, so using default: x-dummy-x
@@ -685,10 +685,10 @@ 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: 9.1
+      total time: 13.2
 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/159476/meta.yaml --n-max-queries 100
+run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/349339/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]
@@ -699,12 +699,12 @@ 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/159476 --input-metafname /tmp/runner/hmms/159476/meta.yaml --n-max-queries 100
+run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/349339 --input-metafname /tmp/runner/hmms/349339/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/159476/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/349339/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
+    igh:   49 / 100 v annotations (51 failed) with 28 v genes in 0.2 sec
     igk:   40 / 100 v annotations (60 failed) with 18 v genes in 0.2 sec
     igl:   15 / 100 v annotations (85 failed) with 12 v genes in 0.1 sec
 totals: igh 48 igk 37 igl 15
@@ -724,10 +724,10 @@ 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/159476/
-  igh: 48 to 159476/igh.fa
-  igk: 37 to 159476/igk.fa
-  igl: 15 to 159476/igl.fa
+writing to /tmp/runner/hmms/349339/
+  igh: 48 to 349339/igh.fa
+  igk: 37 to 349339/igk.fa
+  igl: 15 to 349339/igl.fa
 writing to paired subdirs
     igh+igk:
       igh: 36 / 48 to igh+igk/igh.fa
@@ -736,107 +736,107 @@ 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/159476/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/159476/meta.yaml
-  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/159476/meta.yaml: paired-uids
+run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/349339/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/349339/meta.yaml
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/349339/meta.yaml: paired-uids
 caching parameters
-  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.1 sec
+  vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.2 sec
     keeping 23 / 198 v genes
 smith-waterman  (new-allele fitting)
   vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.1 sec
     running 10 procs for 48 seqs
       info for 48 / 48 = 1.000   (removed: 0 failed)
       kept 1 (0.021) unproductive
-    water time: 0.2  (ig-sw 0.0  processing 0.2)
+    water time: 0.3  (ig-sw 0.1  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.2 sec
+  vsearch: 48 / 48 v annotations (0 failed) with 23 v genes in 0.1 sec
     running 10 procs for 48 seqs
       info for 48 / 48 = 1.000   (removed: 0 failed)
       kept 1 (0.021) unproductive
         writing sw results to test/paired/new-results/test/parameters/data/igh/sw-cache.yaml
-    writing parameters to test/paired/new-results/test/parameters/data/igh/sw (2.7 sec)
-    water time: 3.0  (ig-sw 2.8  processing 0.2)
+    writing parameters to test/paired/new-results/test/parameters/data/igh/sw (6.9 sec)
+    water time: 7.4  (ig-sw 7.1  processing 0.2)
   writing hmms     removed 13 genes from glfo (leaving v 23  d 19  j 6)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(1.9 sec)
+(2.7 sec)
 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 (2.6 sec)
-         infra time: 2.8
-      hmm step time: 3.7
+    writing parameters to test/paired/new-results/test/parameters/data/igh/hmm (4.3 sec)
+         infra time: 4.5
+      hmm step time: 6.0
   writing hmms     removed 1  genes from glfo (leaving v 23  d 18  j 6)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(1.9 sec)
-      total time: 11.3
+(2.3 sec)
+      total time: 19.6
 cache-parameters igk:
-run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/159476/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/159476/meta.yaml
-  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/159476/meta.yaml: paired-uids
+run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/349339/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/349339/meta.yaml
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/349339/meta.yaml: paired-uids
 caching parameters
-  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.2 sec
+  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
     keeping 16 / 64 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.2 sec
+  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
     running 10 procs for 37 seqs
       info for 37 / 37 = 1.000   (removed: 0 failed)
       kept 1 (0.027) unproductive
-    water time: 0.2  (ig-sw 0.0  processing 0.1)
+    water time: 0.2  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.3 sec
+  vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.1 sec
     running 10 procs for 37 seqs
       info for 37 / 37 = 1.000   (removed: 0 failed)
       kept 1 (0.027) unproductive
         writing sw results to test/paired/new-results/test/parameters/data/igk/sw-cache.yaml
-    writing parameters to test/paired/new-results/test/parameters/data/igk/sw (2.0 sec)
-    water time: 2.3  (ig-sw 2.1  processing 0.1)
+    writing parameters to test/paired/new-results/test/parameters/data/igk/sw (2.9 sec)
+    water time: 3.2  (ig-sw 3.0  processing 0.2)
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(1.2 sec)
+(2.7 sec)
 hmm
     reading output
         read 37 hmm output lines with 37 sequences in 37 events  (0 failures)
-    writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (1.8 sec)
-         infra time: 1.9
-      hmm step time: 2.4
+    writing parameters to test/paired/new-results/test/parameters/data/igk/hmm (3.4 sec)
+         infra time: 3.6
+      hmm step time: 4.2
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(1.2 sec)
-      total time: 8.1
+(1.5 sec)
+      total time: 12.3
 cache-parameters igl:
-run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/159476/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/159476/meta.yaml
-  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/159476/meta.yaml: paired-uids
+run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/349339/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/349339/meta.yaml
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/349339/meta.yaml: paired-uids
 caching parameters
-  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.2 sec
+  vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.1 sec
     keeping 10 / 80 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 15 / 15 v annotations (0 failed) with 10 v genes in 0.2 sec
+  vsearch: 15 / 15 v annotations (0 failed) with 10 v genes in 0.1 sec
     running 10 procs for 15 seqs
       info for 15 / 15 = 1.000   (removed: 0 failed)
-    water time: 0.2  (ig-sw 0.0  processing 0.1)
+    water time: 0.2  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
   vsearch: 15 / 15 v annotations (0 failed) with 10 v genes in 0.2 sec
     running 10 procs for 15 seqs
       info for 15 / 15 = 1.000   (removed: 0 failed)
         writing sw results to test/paired/new-results/test/parameters/data/igl/sw-cache.yaml
-    writing parameters to test/paired/new-results/test/parameters/data/igl/sw (1.3 sec)
-    water time: 1.5  (ig-sw 1.4  processing 0.2)
+    writing parameters to test/paired/new-results/test/parameters/data/igl/sw (1.5 sec)
+    water time: 1.8  (ig-sw 1.6  processing 0.2)
   writing hmms     removed 6  genes from glfo (leaving v 10  d 1  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.7 sec)
+(1.0 sec)
 hmm
     reading output
         read 15 hmm output lines with 15 sequences in 15 events  (0 failures)
-    writing parameters to test/paired/new-results/test/parameters/data/igl/hmm (1.5 sec)
-         infra time: 1.6
-      hmm step time: 1.9
+    writing parameters to test/paired/new-results/test/parameters/data/igl/hmm (2.0 sec)
+         infra time: 2.1
+      hmm step time: 2.5
   writing hmms     removed 0  genes from glfo (leaving v 10  d 1  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.7 sec)
-      total time: 5.6
-      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/159476/: failed.fa
-      total time: 32.2
+(0.9 sec)
+      total time: 6.9
+      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/349339/: failed.fa
+      total time: 50.0