partis-bcr 1.0.12__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl

test/paired/new-results/subset-partition-new-simu/isub-1/partition.log

@@ -36,45 +36,45 @@ writing to paired subdirs
 run partis cache-parameters --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
   --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
 caching parameters
-  vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.1 sec
+  vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.2 sec
     keeping 6 / 198 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
+  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
     running 10 procs for 32 seqs
       info for 32 / 32 = 1.000   (removed: 0 failed)
       kept 14 (0.438) unproductive
-    water time: 0.2  (ig-sw 0.0  processing 0.2)
+    water time: 0.2  (ig-sw 0.1  processing 0.2)
 smith-waterman  (writing parameters)
   vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
     running 10 procs for 32 seqs
       info for 32 / 32 = 1.000   (removed: 0 failed)
       kept 14 (0.438) unproductive
         writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.9 sec)
-    water time: 1.2  (ig-sw 1.0  processing 0.2)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (1.5 sec)
+    water time: 1.9  (ig-sw 1.7  processing 0.2)
   writing hmms     removed 18 genes from glfo (leaving v 6  d 16  j 4)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.8 sec)
+(1.3 sec)
 hmm
     reading output
         read 32 hmm output lines with 32 sequences in 32 events  (0 failures)
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.8 sec)
-         infra time: 0.9
-      hmm step time: 1.6
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (1.4 sec)
+         infra time: 1.5
+      hmm step time: 3.7
   writing hmms     removed 3  genes from glfo (leaving v 6  d 13  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: 4.8
+(0.9 sec)
+      total time: 8.8
 cache-parameters igk:
 run partis cache-parameters --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
   --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
 caching parameters
-  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
     keeping 5 / 64 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
     running 10 procs for 18 seqs
       info for 18 / 18 = 1.000   (removed: 0 failed)
       kept 9 (0.500) unproductive
@@ -85,23 +85,23 @@ smith-waterman  (writing parameters)
       info for 18 / 18 = 1.000   (removed: 0 failed)
       kept 9 (0.500) unproductive
         writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.8 sec)
-    water time: 1.1  (ig-sw 0.9  processing 0.2)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (1.2 sec)
+    water time: 1.5  (ig-sw 1.3  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
-(0.5 sec)
+(0.6 sec)
 hmm
     reading output
         read 18 hmm output lines with 18 sequences in 18 events  (0 failures)
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.8 sec)
-         infra time: 0.9
-      hmm step time: 1.2
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (1.1 sec)
+         infra time: 1.2
+      hmm step time: 1.6
   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: 3.8
+(0.6 sec)
+      total time: 5.0
 cache-parameters igl:
 run partis cache-parameters --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
   --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -120,48 +120,48 @@ smith-waterman  (writing parameters)
       info for 11 / 11 = 1.000   (removed: 0 failed)
       kept 7 (0.636) unproductive
         writing sw results to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.5 sec)
-    water time: 0.8  (ig-sw 0.6  processing 0.2)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.8 sec)
+    water time: 1.0  (ig-sw 0.9  processing 0.2)
   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)
+(0.5 sec)
 hmm
     reading output
         read 11 hmm output lines with 11 sequences in 11 events  (0 failures)
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.4 sec)
-         infra time: 0.5
-      hmm step time: 0.7
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm (0.6 sec)
+         infra time: 0.7
+      hmm step time: 1.1
   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: 2.5
+(0.3 sec)
+      total time: 3.7
 partition igh:
 run partis partition --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
   --input-metafnames: added meta info for 32 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
 partitioning     (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
 smith-waterman
-  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.2 sec
+  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.1 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
       info for 32 / 32 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 14 (0.438) unproductive
         water time: 0.0
 hmm
-  caching all 32 naive sequences (0.7s)
+  caching all 32 naive sequences (1.1s)
     collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
-  30 clusters with 10 procs (0.4s)
-   29 clusters with 7 procs (0.5s)
+  30 clusters with 10 procs (0.5s)
+   29 clusters with 7 procs (0.6s)
    28 clusters with 5 procs (0.5s)
-   28 clusters with 3 procs (0.5s)
-   23 clusters with 2 procs (0.5s)
-   20 clusters with 1 proc (0.9s)
+   28 clusters with 3 procs (0.7s)
+   23 clusters with 2 procs (0.8s)
+   20 clusters with 1 proc (1.1s)
    note not merging entire cpath history
-      partition loop time: 3.2
+      partition loop time: 4.2
 getting annotations for final partition
-  subcluster annotating 16 clusters with steps:  (0.5s) (0.2s) 
-    subcluster annotation time 0.7
-      total time: 4.9
+  subcluster annotating 16 clusters with steps:  (0.9s) (0.3s) 
+    subcluster annotation time 1.2
+      total time: 6.7
 partition igk:
 run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
   --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -173,19 +173,19 @@ smith-waterman
       kept 9 (0.500) unproductive
         water time: 0.0
 hmm
-  caching all 18 naive sequences (0.4s)
+  caching all 18 naive sequences (0.5s)
     collapsed 18 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 3 procs (0.2s)
-   6 clusters with 2 procs (0.1s)
-   6 clusters with 1 proc (0.4s)
-       partition loop time: 1.3
+   7 clusters with 3 procs (0.3s)
+   6 clusters with 2 procs (0.2s)
+   6 clusters with 1 proc (0.5s)
+       partition loop time: 1.6
 getting annotations for final partition
-  subcluster annotating 6 clusters with steps:  (0.3s) (0.1s) 
+  subcluster annotating 6 clusters with steps:  (0.4s) (0.1s) 
     subcluster annotation time 0.5
-      total time: 2.4
+      total time: 2.7
 partition igl:
 run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
   --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
@@ -197,17 +197,17 @@ smith-waterman
       kept 7 (0.636) unproductive
         water time: 0.0
 hmm
-  caching all 11 naive sequences (0.3s)
+  caching all 11 naive sequences (0.5s)
     collapsed 11 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 3 procs (0.3s)
    3 clusters with 2 procs (0.2s)
    3 clusters with 1 proc (0.3s)
-       partition loop time: 0.6
+       partition loop time: 0.7
 getting annotations for final partition
-  subcluster annotating 3 clusters with steps:  (0.2s) (0.1s) 
-    subcluster annotation time 0.3
-      total time: 1.4
+  subcluster annotating 3 clusters with steps:  (0.3s) (0.2s) 
+    subcluster annotation time 0.4
+      total time: 1.8
 combining chains
 cleaning pair info for 61 seqs
      synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0  k 0  l 0
@@ -227,24 +227,22 @@ cleaning pair info for 61 seqs
        k            0           0           1
   merge time 0.0
   need to get annotations for 2/11 joint igh clusters
-     tag: v1.0.12
 annotate igh+igk: igh
 run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
   --input-metafnames: added meta info for 19 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml: loci paired-uids
   --input-partition-fname: read best partition with 19 sequences in 11 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
 smith-waterman
-  vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.1 sec
+  vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.2 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
       info for 19 / 19 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 7 (0.368) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 11 clusters with steps:  (0.6s) (0.2s) 
-    subcluster annotation time 0.8
-      total time: 0.8
+  subcluster annotating 11 clusters with steps:  (0.7s) (0.2s) 
+    subcluster annotation time 0.9
+      total time: 1.1
   need to get annotations for 6/11 joint igk clusters
-     tag: v1.0.12
 annotate igh+igk: igk
 run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
   --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml: loci paired-uids
@@ -259,8 +257,9 @@ smith-waterman
 hmm
     reading output
         read 11 hmm output lines with 18 sequences in 11 events  (0 failures)
-      hmm step time: 0.4
-      total time: 0.5
+         infra time: 0.1
+      hmm step time: 0.5
+      total time: 0.6
 igh+igl: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2  l 1
             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
@@ -277,7 +276,6 @@ hmm
        l            0           0           1
   merge time 0.0
   need to get annotations for 2/5 joint igh clusters
-     tag: v1.0.12
 annotate igh+igl: igh
 run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
   --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -290,11 +288,10 @@ smith-waterman
       kept 7 (0.583) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 5 clusters with steps:  (0.4s) (0.3s) 
-    subcluster annotation time 0.7
-      total time: 0.8
+  subcluster annotating 5 clusters with steps:  (0.4s) (0.4s) 
+    subcluster annotation time 0.8
+      total time: 1.0
   need to get annotations for 5/5 joint igl clusters
-     tag: v1.0.12
 annotate igh+igl: igl
 run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
   --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
@@ -307,7 +304,7 @@ smith-waterman
       kept 7 (0.636) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 5 clusters with steps:  (0.2s) (0.3s) 
+  subcluster annotating 5 clusters with steps:  (0.4s) (0.2s) 
     subcluster annotation time 0.5
       total time: 0.6
   --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
@@ -322,4 +319,4 @@ hmm
         h   16 --> 16  
         k    6 --> 11   +5
         l    3 --> 5    +2
-      total time: 47.7
+      total time: 66.7

test/paired/new-results/subset-partition-new-simu/merged-partition.log

@@ -17,7 +17,7 @@ partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/
     removed 3/56 queries from input info that were absent from input partition
 partitioning     (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
 smith-waterman
-  vsearch: 53 / 53 v annotations (0 failed) with 6 v genes in 0.1 sec
+  vsearch: 53 / 53 v annotations (0 failed) with 6 v genes in 0.2 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
       info for 53 / 53 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 24 (0.453) unproductive
@@ -27,16 +27,16 @@ hmm
     caching input annotation naive seqs in bcrham cache file for 27 clusters (53 seqs)
       --continue-from-input-partition: using input partition for initial cpath
              27 clusters (53 seqs)
-  27 clusters with 10 procs (0.6s)
-   26 clusters with 7 procs (0.6s)
-   23 clusters with 5 procs (0.5s)
-   22 clusters with 3 procs (0.5s)
+  27 clusters with 10 procs (0.9s)
+   26 clusters with 7 procs (0.7s)
+   23 clusters with 5 procs (0.6s)
+   22 clusters with 3 procs (0.6s)
    21 clusters with 2 procs (0.4s)
-   21 clusters with 1 proc (0.7s)
-       partition loop time: 3.1
+   21 clusters with 1 proc (0.9s)
+       partition loop time: 4.1
 getting annotations for final partition
-  subcluster annotating 18 clusters with steps:  (0.8s) (0.4s) (0.3s) 
-    subcluster annotation time 1.6
+  subcluster annotating 18 clusters with steps:  (1.0s) (0.4s) (0.3s) 
+    subcluster annotation time 1.7
     warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
@@ -47,7 +47,7 @@ getting annotations for final partition
     warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 56 missing ids as singletons to inferred partition, to match ids in true partition
-      total time: 4.9
+      total time: 6.3
 partition igk:
 run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --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/partition-igk.yaml --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml
   warning replacing 'paired-uids'/'paired-uids' value for 'bc11af4843-igk' with value from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml: ['bc11af4843-igh', 'eee6809ad6-igh', 'eee6809ad6-igl'] --> ['eee6809ad6-igh']
@@ -74,16 +74,16 @@ hmm
       --continue-from-input-partition: using input partition for initial cpath
              19 clusters (36 seqs)
   19 clusters with 10 procs (0.3s)
-   17 clusters with 7 procs (0.4s)
-   15 clusters with 5 procs (0.3s)
+   17 clusters with 7 procs (0.3s)
+   15 clusters with 5 procs (0.2s)
    12 clusters with 3 procs (0.2s)
-   11 clusters with 2 procs (0.3s)
+   11 clusters with 2 procs (0.2s)
    7 clusters with 1 proc (0.4s)
    note not merging entire cpath history
-      partition loop time: 1.8
+      partition loop time: 1.6
 getting annotations for final partition
-  subcluster annotating 6 clusters with steps:  (0.4s) (0.2s) (0.2s) 
-    subcluster annotation time 0.8
+  subcluster annotating 6 clusters with steps:  (0.5s) (0.3s) (0.1s) 
+    subcluster annotation time 0.9
       total time: 2.9
 partition igl:
 run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --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/partition-igl.yaml --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/ref-results/test/simu/igl.yaml --outfname test/paired/new-results/subset-partition-new-simu/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
@@ -114,14 +114,14 @@ hmm
              8 clusters (18 seqs)
   reducing n procs to number of clusters: 10 --> 8
   8 clusters with 8 procs (0.3s)
-   8 clusters with 6 procs (0.2s)
-   7 clusters with 4 procs (0.2s)
+   8 clusters with 6 procs (0.3s)
+   7 clusters with 4 procs (0.3s)
    6 clusters with 3 procs (0.2s)
-   6 clusters with 2 procs (0.3s)
+   6 clusters with 2 procs (0.2s)
    3 clusters with 1 proc (0.3s)
-       partition loop time: 1.5
+       partition loop time: 1.6
 getting annotations for final partition
-  subcluster annotating 3 clusters with steps:  (0.3s) (0.2s) (0.2s) 
+  subcluster annotating 3 clusters with steps:  (0.3s) (0.2s) (0.1s) 
     subcluster annotation time 0.7
     warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
@@ -129,7 +129,7 @@ getting annotations for final partition
     warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
     warning added 3 / 21 missing ids as singletons to inferred partition, to match ids in true partition
-      total time: 2.4
+      total time: 2.5
 combining chains
 cleaning pair info for 107 seqs
      synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0  k 0  l 0
@@ -165,7 +165,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
        joint   0.963  0.594
   merge time 0.0
   need to get annotations for 6/15 joint igh clusters
-     tag: v1.0.12
 annotate igh+igk: igh
     removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
 run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -173,17 +172,16 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
   --input-partition-fname: read best partition with 35 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm)
 smith-waterman
-  vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.1 sec
+  vsearch: 35 / 35 v annotations (0 failed) with 5 v genes in 0.2 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml
       info for 35 / 35 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 13 (0.371) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 15 clusters with steps:  (0.5s) (0.2s) 
-    subcluster annotation time 0.8
-      total time: 1.0
+  subcluster annotating 15 clusters with steps:  (0.7s) (0.3s) 
+    subcluster annotation time 1.0
+      total time: 1.3
   need to get annotations for 13/15 joint igk clusters
-     tag: v1.0.12
 annotate igh+igk: igk
     removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
 run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -191,15 +189,15 @@ hmm
   --input-partition-fname: read best partition with 36 sequences in 15 clusters from test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/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 0.2 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/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
 hmm
-  subcluster annotating 15 clusters with steps:  (0.6s) (0.2s) 
-    subcluster annotation time 0.7
-      total time: 0.9
+  subcluster annotating 15 clusters with steps:  (0.7s) (0.2s) 
+    subcluster annotation time 0.9
+      total time: 1.2
 igh+igl: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 3 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 2  l 1
             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
@@ -228,7 +226,6 @@ hmm
        joint   1.000  0.787
   merge time 0.0
   need to get annotations for 2/6 joint igh clusters
-     tag: v1.0.12
 annotate igh+igl: igh
     removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
 run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -242,11 +239,10 @@ smith-waterman
       kept 11 (0.579) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 6 clusters with steps:  (0.5s) (0.3s) (0.3s) 
-    subcluster annotation time 1.0
+  subcluster annotating 6 clusters with steps:  (0.4s) (0.3s) (0.4s) 
+    subcluster annotation time 1.1
       total time: 1.2
   need to get annotations for 6/6 joint igl clusters
-     tag: v1.0.12
 annotate igh+igl: igl
     removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
 run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igl.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml --ignore-sw-pair-info
@@ -254,7 +250,7 @@ hmm
   --input-partition-fname: read best partition with 18 sequences in 6 clusters from test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm)
 smith-waterman
-  vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.2 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 3 v genes in 0.1 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml
       info for 18 / 18 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 13 (0.722) unproductive
@@ -262,7 +258,7 @@ smith-waterman
 hmm
   subcluster annotating 6 clusters with steps:  (0.3s) (0.2s) (0.2s) 
     subcluster annotation time 0.7
-      total time: 0.9
+      total time: 0.8
   --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml
   concatenating heavy chain loci:
       h starting with 15 annotations (35 seqs)
@@ -276,4 +272,4 @@ hmm
         h   18 --> 21   +3
         k    6 --> 15   +9
         l    3 --> 6    +3
-      total time: 30.4
+      total time: 36.4