partis-bcr 1.0.13__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl

test/new-results/test.log

@@ -10,32 +10,32 @@ smith-waterman  (new-allele fitting)
     running 11 procs for 1 seq
       info for 36 / 36 = 1.000   (removed: 0 failed)
       kept 18 (0.500) unproductive
-    water time: 0.4  (ig-sw 0.0  processing 0.1)
+    water time: 0.3  (ig-sw 0.0  processing 0.1)
 smith-waterman  (writing parameters)
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
     running 10 procs for 36 seqs
     running 11 procs for 1 seq
       info for 36 / 36 = 1.000   (removed: 0 failed)
       kept 18 (0.500) unproductive
         writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
-    writing parameters to test/new-results/test/parameters/simu/sw (1.2 sec)
-    water time: 1.6  (ig-sw 1.3  processing 0.2)
+    writing parameters to test/new-results/test/parameters/simu/sw (0.9 sec)
+    water time: 1.3  (ig-sw 1.0  processing 0.2)
   writing hmms     removed 30 genes from glfo (leaving v 7  d 5  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.7 sec)
+(0.6 sec)
 hmm
     reading output
         read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/simu/hmm (1.5 sec)
-    writing parameters to test/new-results/test/parameters/simu/true (1.4 sec)
-         infra time: 3.0
-      hmm step time: 3.9
+    writing parameters to test/new-results/test/parameters/simu/hmm (0.8 sec)
+    writing parameters to test/new-results/test/parameters/simu/true (0.8 sec)
+         infra time: 1.8
+      hmm step time: 2.3
   writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.8 sec)
-      total time: 7.9
+(0.6 sec)
+      total time: 5.7
 annotate-new-simu                partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --is-simu --plotdir test/new-results/annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/annotate-new-simu.yaml
 annotating    (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
@@ -46,71 +46,70 @@ smith-waterman
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-        water time: 0.2
+        water time: 0.1
 hmm
     reading output
         read 36 hmm output lines with 36 sequences in 36 events  (0 failures)
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-         infra time: 0.1
-      hmm step time: 1.0
-      total time: 1.3
+      hmm step time: 0.7
+      total time: 0.9
 multi-annotate-new-simu          partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --simultaneous-true-clonal-seqs --is-simu --plotdir test/new-results/multi-annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/multi-annotate-new-simu.yaml
 annotating    (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
   note: not running msa indel stuff for --simultaneous-true-clonal-seqs, so any families with shm indels within cdr3 will be split up before running the hmm. To fix this you'll either need to run set_msa_info() (which is fine and easy, but slow, and requires deciding whether to make sure to run parameter caching with the arg, or else rerun smith waterman with the msa indels
         reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 18 (0.500) unproductive
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
-(0.1 sec)
-        water time: 0.3
+(0.0 sec)
+        water time: 0.1
 hmm
   --simultaneous-true-clonal-seqs: grouping seqs according to true partition
   warning split apart 1 cluster that contained multiple cdr3 lengths (total clusters: 10 --> 11)
       cluster splits:   8 --> 7 1
-  subcluster annotating 11 clusters with steps:  (0.8s) (0.2s)   plotting performance 
+  subcluster annotating 11 clusters with steps:  (0.4s) (0.2s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
 
-    subcluster annotation time 1.1
-      total time: 1.5
+    subcluster annotation time 0.7
+      total time: 1.0
 partition-new-simu               partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --plotdir test/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml
 partitioning     (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
         reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 18 (0.500) unproductive
   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
-        water time: 0.2
+        water time: 0.1
 hmm
   --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
-  caching all 36 naive sequences (1.0s)
+  caching all 36 naive sequences (0.5s)
     collapsed 36 queries into 12 clusters with identical naive seqs (0.0 sec)
-  12 clusters with 10 procs (0.4s)
-   12 clusters with 7 procs (0.2s)
+  12 clusters with 10 procs (0.3s)
+   12 clusters with 7 procs (0.3s)
    12 clusters with 5 procs (0.2s)
    12 clusters with 3 procs (0.2s)
    12 clusters with 2 procs (0.3s)
-   11 clusters with 1 proc (0.6s)
-       partition loop time: 1.9
+   11 clusters with 1 proc (0.5s)
+       partition loop time: 1.8
 getting annotations for final partition
-  subcluster annotating 10 clusters with steps:  (0.6s) (0.2s) (0.2s)   plotting performance 
+  subcluster annotating 10 clusters with steps:  (0.4s) (0.2s) (0.3s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
 (0.0 sec)
 
-    subcluster annotation time 1.1
-      total time: 4.5
+    subcluster annotation time 0.9
+      total time: 3.6
 seed-partition-new-simu          partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --max-ccf-fail-frac 0.10 --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --seed-unique-id 8024ed1a22 --random-seed 1 --n-procs 10 --outfname test/new-results/seed-partition-new-simu.yaml
 partitioning     (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
         reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 18 (0.500) unproductive
@@ -123,17 +122,17 @@ hmm
   2 clusters with 2 procs (0.2s)
        removed 0 sequences in unseeded clusters, split 2 seeded clusters into 11 singletons, and merged these into 2 clusters with identical naive seqs (0.0 sec)
         new n_procs 1 (initial seqs/proc: 5.50   new seqs/proc: 2.00
-  2 clusters with 1 proc (0.2s)
-       partition loop time: 0.4
+  2 clusters with 1 proc (0.1s)
+       partition loop time: 0.3
 getting annotations for final partition
-  subcluster annotating 1 cluster with steps:  (0.3s) (0.2s) (0.2s) 
-    subcluster annotation time 0.6
+  subcluster annotating 1 cluster with steps:  (0.2s) (0.2s) (0.1s) 
+    subcluster annotation time 0.5
   seed cluster size in best partition: 11, excluding seed seq: 10
-      total time: 1.3
+      total time: 1.2
 vsearch-partition-new-simu       partis partition --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --naive-vsearch --is-simu --persistent-cachefname test/new-results/cache-new-partition.csv --random-seed 1 --n-procs 10 --outfname test/new-results/vsearch-partition-new-simu.yaml
 partitioning     (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
-  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.2 sec
+  vsearch: 36 / 36 v annotations (0 failed) with 7 v genes in 0.1 sec
         reading sw results from test/new-results/test/parameters/simu/sw-cache.yaml
       info for 36 / 36 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 18 (0.500) unproductive
@@ -143,12 +142,12 @@ hmm
         collapsed 36 sequences (36 initial naive seqs/clusters) into 12 unique naive sequences over 9 cdr3 lengths (0.0 sec)
     using hfrac bound for vsearch 0.013
     running vsearch 9 times (once for each cdr3 length class): . . . . . . . . . 
-      vsearch time: 0.2
+      vsearch time: 0.3
 getting annotations for final partition
       calculating hmm annotations even though --fast/--naive-vsearch was set (you can set --use-sw-annotations to get faster (but substantially less accurate) annotations, or set --dont-calculate-annotations if you only need the partition)
-  subcluster annotating 10 clusters with steps:  (0.6s) (0.2s) (0.2s) 
-    subcluster annotation time 1.0
-      total time: 1.6
+  subcluster annotating 10 clusters with steps:  (0.4s) (0.2s) (0.1s) 
+    subcluster annotation time 0.8
+      total time: 1.4
 get-selection-metrics-new-simu   partis get-selection-metrics --dont-write-git-info --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --outfname test/new-results/partition-new-simu.yaml --selection-metric-fname test/new-results/get-selection-metrics-new-simu.yaml
   note: --parameter-dir not set, so using default: x-dummy-x
   note: By default we print/operate on *all* annotations in the output file, which in general can include annotations from non-best partititons and non-seed clusters (e.g. if --n-final-clusters was set).
@@ -160,7 +159,7 @@ getting annotations for final partition
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
         run /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out /Users/runner/work/partis/partis/test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
-      made 3 fasttree trees (0.5s)
+      made 3 fasttree trees (0.3s)
     tree origins: 3 ran fasttree
     skipped 1/4 clusters smaller than 4
       setting default tau to 1 / 352 = 0.0028
@@ -172,7 +171,7 @@ getting annotations for final partition
       warning get_aa_tree() (AA inf tree, iclust 2): skipped 11/13 edges for which we didn't have sequences for both nodes (i.e. left the original branch length unmodified). Missing nodes: apr dhq eyz fnv nox
     skipped 1/4 clusters that had no uids in common with tree
   writing selection metrics to test/new-results/get-selection-metrics-new-simu.yaml
-      total time: 0.7
+      total time: 0.4
 cache-parameters-data            partis cache-parameters --dont-write-git-info --infname test/mishmash.fa --parameter-dir test/new-results/test/parameters/data --sw-cachefname test/new-results/test/parameters/data/sw-cache.yaml --n-max-queries 50 --input-metafnames test/input-meta.yaml --random-seed 1 --n-procs 10
     stopped after reading 50 sequences from test/mishmash.fa
   --n-max-queries: stopped after reading 50 queries from input file
@@ -181,33 +180,33 @@ caching parameters
   vsearch: 44 / 50 v annotations (6 failed) with 54 v genes in 0.2 sec
     keeping 24 / 198 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.2 sec
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.1 sec
     running 10 procs for 50 seqs
     running 12 procs for 5 seqs
       info for 46 / 50 = 0.920   (removed: 4 failed)
       kept 16 (0.320) unproductive
     water time: 0.4  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.2 sec
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.1 sec
     running 10 procs for 46 seqs
     running 11 procs for 1 seq
       info for 46 / 50 = 0.920   (removed: 4 failed)
       kept 16 (0.320) unproductive
         writing sw results to test/new-results/test/parameters/data/sw-cache.yaml
-    writing parameters to test/new-results/test/parameters/data/sw (2.1 sec)
-    water time: 2.5  (ig-sw 2.2  processing 0.1)
+    writing parameters to test/new-results/test/parameters/data/sw (1.2 sec)
+    water time: 1.6  (ig-sw 1.3  processing 0.1)
   writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(2.4 sec)
+(1.6 sec)
 hmm
     reading output
         read 46 hmm output lines with 46 sequences in 46 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/data/hmm (1.7 sec)
-         infra time: 1.8
-      hmm step time: 4.2
+    writing parameters to test/new-results/test/parameters/data/hmm (1.0 sec)
+         infra time: 1.1
+      hmm step time: 2.2
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(1.8 sec)
-      total time: 12.0
+(1.4 sec)
+      total time: 7.8

test/paired/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 32 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
-Total branch-length 0.172 after 0.01 sec
+Total branch-length 0.172 after 0.00 sec
 ML-NNI round 1: LogLk = -1718.230 NNIs 0 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2101 0.3021 0.2760 0.2118
 GTR rates(ac ag at cg ct gt) 1.2927 1.2254 1.4006 0.7465 1.0327 1.0000
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.666 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.06
+ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.04
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.08 (final)
-Optimize all lengths: LogLk = -1660.925 Time 0.08
-Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -1660.925 Time 0.05
+Total time: 0.06 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-1/log

@@ -8,7 +8,7 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Ignored unknown character X (seen 176 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
-Total branch-length 0.116 after 0.01 sec
+Total branch-length 0.116 after 0.00 sec
 ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2498 0.2482 0.2788 0.2231
 GTR rates(ac ag at cg ct gt) 0.7182 0.4393 0.9759 0.8068 0.8119 1.0000
@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.652 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04
+ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.05 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.06
-Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.05
+Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.641 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -1274.638 Time 0.04
-Total time: 0.05 seconds Unique: 6/6 Bad splits: 0/3
+ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -1274.638 Time 0.03
+Total time: 0.04 seconds Unique: 6/6 Bad splits: 0/3

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.678 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -968.458 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -968.458 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -968.417 Time 0.04
-Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5
+Optimize all lengths: LogLk = -968.417 Time 0.03
+Total time: 0.03 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log

@@ -9,7 +9,7 @@ Ignored unknown character X (seen 21 times)
 Initial topology in 0.00 seconds
 Refining topology: 11 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
 Total branch-length 0.133 after 0.00 sec
-ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.01
+ML-NNI round 1: LogLk = -824.130 NNIs 0 max delta 0.00 Time 0.00
 GTR Frequencies: 0.2278 0.2456 0.3207 0.2059
 GTR rates(ac ag at cg ct gt) 1.1354 1.3036 0.8502 1.1285 0.5919 1.0000
 Switched to using 20 rate categories (CAT approximation)
@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -794.353 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -794.321 Time 0.03
-Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4
+ML-NNI round 3: LogLk = -794.321 NNIs 0 max delta 0.00 Time 0.02 (final)
+Optimize all lengths: LogLk = -794.321 Time 0.02
+Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4

test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log

@@ -19,5 +19,5 @@ Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00 (final)
-Optimize all lengths: LogLk = -457.145 Time 0.01
+Optimize all lengths: LogLk = -457.145 Time 0.00
 Total time: 0.01 seconds Unique: 3/8 Bad splits: 0/0

test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log

@@ -19,5 +19,5 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -455.146 NNIs 0 max delta 0.00 Time 0.00
 Turning off heuristics for final round of ML NNIs (converged)
-Optimize all lengths: LogLk = -455.146 Time 0.01
+Optimize all lengths: LogLk = -455.146 Time 0.00
 Total time: 0.01 seconds Unique: 2/8 Bad splits: 0/0

test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log

@@ -15,8 +15,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.695 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -1077.707 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -1077.702 Time 0.04
-Total time: 0.06 seconds Unique: 9/9 Bad splits: 0/6
+ML-NNI round 3: LogLk = -1077.702 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -1077.702 Time 0.03
+Total time: 0.04 seconds Unique: 9/9 Bad splits: 0/6

test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log

@@ -8,15 +8,15 @@ ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
 Total branch-length 0.074 after 0.00 sec
-ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.01
+ML-NNI round 1: LogLk = -630.173 NNIs 0 max delta 0.00 Time 0.00
 GTR Frequencies: 0.2044 0.3132 0.2728 0.2096
 GTR rates(ac ag at cg ct gt) 0.8954 1.2357 1.0576 0.3959 0.3435 1.0000
 Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.641 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -613.260 Time 0.03
-Total time: 0.04 seconds Unique: 8/9 Bad splits: 0/5
+ML-NNI round 3: LogLk = -613.260 NNIs 0 max delta 0.00 Time 0.02 (final)
+Optimize all lengths: LogLk = -613.260 Time 0.02
+Total time: 0.03 seconds Unique: 8/9 Bad splits: 0/5