partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

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

@@ -1,7 +1,7 @@
 partis partition --dont-write-git-info --paired-loci --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu/isub-1 --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/input-seqs.fa
   note: found 'paired-uids' in --input-metafnames, so not extracting pairing info
 run split-loci.py test/paired/new-results/subset-partition-new-simu/isub-1/input-seqs.fa --outdir test/paired/new-results/subset-partition-new-simu/isub-1 --input-metafname test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
-  --input-metafnames: added meta info for 61 sequences from /Users/runner/work/partis/partis/test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
+  --input-metafnames: added meta info for 61 sequences from /home/runner/work/partis/partis/test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml: loci paired-uids
     read pairing info for 61 seqs from input meta file
     read loci for 61 sequences from input meta file (so not running vsearch)
 totals: igh 32 igk 18 igl 11
@@ -36,138 +36,126 @@ 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 0.2 sec
+  vsearch: 32 / 32 v annotations (0 failed) with 8 v genes in 0.0 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 0.0 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: 0.1  (ig-sw 0.0  processing 0.0)
 smith-waterman  (writing parameters)
-  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 0.0 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 0.1)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw (0.6 sec)
+    water time: 0.7  (ig-sw 0.6  processing 0.0)
   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)
+(0.5 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: 1.0
-      hmm step time: 1.7
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm (0.5 sec)
+         infra time: 0.6
+      hmm step time: 1.2
   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: 5.0
+(0.5 sec)
+      total time: 3.0
 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 0.2 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
     keeping 5 / 64 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
     running 10 procs for 18 seqs
       info for 18 / 18 = 1.000   (removed: 0 failed)
       kept 9 (0.500) unproductive
-    water time: 0.1  (ig-sw 0.0  processing 0.1)
+    water time: 0.0  (ig-sw 0.0  processing 0.0)
 smith-waterman  (writing parameters)
-  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 0.0 sec
     running 10 procs for 18 seqs
       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: 1.0  (ig-sw 0.9  processing 0.1)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw (0.5 sec)
+    water time: 0.5  (ig-sw 0.5  processing 0.0)
   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)
+(0.2 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 (0.7 sec)
-         infra time: 0.8
-      hmm step time: 1.1
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm (0.4 sec)
+         infra time: 0.5
+      hmm step time: 0.7
   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: 3.7
+(0.2 sec)
+      total time: 1.8
 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
 caching parameters
-  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
+  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
     keeping 3 / 80 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
+  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
     running 10 procs for 11 seqs
       info for 11 / 11 = 1.000   (removed: 0 failed)
       kept 7 (0.636) unproductive
-    water time: 0.1  (ig-sw 0.0  processing 0.1)
+    water time: 0.0  (ig-sw 0.0  processing 0.0)
 smith-waterman  (writing parameters)
-  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
+  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
     running 10 procs for 11 seqs
       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: 0.7  (ig-sw 0.6  processing 0.1)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw (0.3 sec)
+    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)
-
-  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.3 sec)
+(0.1 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 (0.3 sec)
+         infra time: 0.3
+      hmm step time: 0.4
   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
-(0.3 sec)
-      total time: 2.5
+(0.1 sec)
+      total time: 1.2
 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 0.1 sec
+  vsearch: 32 / 32 v annotations (0 failed) with 6 v genes in 0.0 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 (0.6s)
     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 (0.4s)
-   28 clusters with 5 procs (0.5s)
-   28 clusters with 3 procs (0.6s)
-   23 clusters with 2 procs (0.6s)
-   20 clusters with 1 proc (0.7s)
+  30 clusters with 10 procs (0.1s)
+   29 clusters with 7 procs (0.2s)
+   28 clusters with 5 procs (0.2s)
+   28 clusters with 3 procs (0.3s)
+   23 clusters with 2 procs (0.3s)
+   20 clusters with 1 proc (0.5s)
    note not merging entire cpath history
-      partition loop time: 3.2
+      partition loop time: 1.7
 getting annotations for final partition
-  subcluster annotating 16 clusters with steps:  (0.6s) (0.2s) 
-    subcluster annotation time 0.9
-      total time: 5.0
+  subcluster annotating 16 clusters with steps:  (0.5s) (0.1s) 
+    subcluster annotation time 0.6
+      total time: 3.0
 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
 partitioning     (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
 smith-waterman
-  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 0.0 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
       info for 18 / 18 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 9 (0.500) unproductive
@@ -176,38 +164,38 @@ hmm
   caching all 18 naive sequences (0.3s)
     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 (0.3s)
-   6 clusters with 2 procs (0.2s)
-   6 clusters with 1 proc (0.4s)
-       partition loop time: 1.4
+  7 clusters with 7 procs (0.0s)
+   7 clusters with 5 procs (0.1s)
+   7 clusters with 3 procs (0.1s)
+   6 clusters with 2 procs (0.0s)
+   6 clusters with 1 proc (0.2s)
+       partition loop time: 0.4
 getting annotations for final partition
-  subcluster annotating 6 clusters with steps:  (0.3s) (0.2s) 
-    subcluster annotation time 0.5
-      total time: 2.3
+  subcluster annotating 6 clusters with steps:  (0.2s) (0.1s) 
+    subcluster annotation time 0.2
+      total time: 0.9
 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
 partitioning     (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
 smith-waterman
-  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.2 sec
+  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
       info for 11 / 11 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 7 (0.636) unproductive
         water time: 0.0
 hmm
-  caching all 11 naive sequences (0.3s)
+  caching all 11 naive sequences (0.2s)
     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 2 procs (0.2s)
-   3 clusters with 1 proc (0.3s)
-       partition loop time: 0.7
+  3 clusters with 3 procs (0.0s)
+   3 clusters with 2 procs (0.0s)
+   3 clusters with 1 proc (0.1s)
+       partition loop time: 0.2
 getting annotations for final partition
-  subcluster annotating 3 clusters with steps:  (0.2s) (0.2s) 
-    subcluster annotation time 0.4
-      total time: 1.6
+  subcluster annotating 3 clusters with steps:  (0.1s) (0.1s) 
+    subcluster annotation time 0.1
+      total time: 0.6
 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
@@ -227,31 +215,29 @@ 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: v1.0.8
 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 0.2 sec
+  vsearch: 19 / 19 v annotations (0 failed) with 5 v genes in 0.0 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:  (0.5s) (0.1s) 
-    subcluster annotation time 0.6
-      total time: 0.8
+  subcluster annotating 11 clusters with steps:  (0.3s) (0.1s) 
+    subcluster annotation time 0.4
+      total time: 0.5
   need to get annotations for 6/11 joint igk clusters
-     tag: v1.0.8
 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
   --input-partition-fname: read best partition with 18 sequences in 11 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/hmm)
 smith-waterman
-  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 0.0 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml
       info for 18 / 18 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 9 (0.500) unproductive
@@ -259,8 +245,8 @@ 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
+      hmm step time: 0.2
+      total time: 0.3
 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
@@ -277,39 +263,37 @@ hmm
        l            0           0           1
   merge time 0.0
   need to get annotations for 2/5 joint igh clusters
-     tag: v1.0.8
 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
   --input-partition-fname: read best partition with 12 sequences in 5 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/hmm)
 smith-waterman
-  vsearch: 12 / 12 v annotations (0 failed) with 3 v genes in 0.1 sec
+  vsearch: 12 / 12 v annotations (0 failed) with 3 v genes in 0.0 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml
       info for 12 / 12 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 7 (0.583) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 5 clusters with steps:  (0.3s) (0.3s) 
-    subcluster annotation time 0.7
-      total time: 0.8
+  subcluster annotating 5 clusters with steps:  (0.2s) (0.1s) 
+    subcluster annotation time 0.3
+      total time: 0.4
   need to get annotations for 5/5 joint igl clusters
-     tag: v1.0.8
 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
   --input-partition-fname: read best partition with 11 sequences in 5 clusters from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/hmm)
 smith-waterman
-  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.1 sec
+  vsearch: 11 / 11 v annotations (0 failed) with 3 v genes in 0.0 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml
       info for 11 / 11 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 7 (0.636) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 5 clusters with steps:  (0.3s) (0.2s) 
-    subcluster annotation time 0.4
-      total time: 0.6
+  subcluster annotating 5 clusters with steps:  (0.1s) (0.1s) 
+    subcluster annotation time 0.2
+      total time: 0.2
   --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml
   concatenating heavy chain loci:
       h starting with 11 annotations (19 seqs)
@@ -322,4 +306,4 @@ hmm
         h   16 --> 16  
         k    6 --> 11   +5
         l    3 --> 5    +2
-      total time: 46.2
+      total time: 25.1