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

{partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.12
+Version: 1.0.12.post1.dev1
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph

{partis_bcr-1.0.12.dist-info → partis_bcr-1.0.12.post1.dev1.dist-info}/RECORD

@@ -304,16 +304,16 @@ data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
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-partis_bcr-1.0.12.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
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@@ -379,9 +379,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
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@@ -506,10 +506,10 @@ test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=qokRc
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@@ -974,8 +974,8 @@ test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv,sha256
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@@ -990,23 +990,23 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.csv,sha256=6H8vsJkv89E5OaepY5bg1DnptEIePK6-C6QjuaBRXv4,337
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.csv,sha256=tzXelx5oSqhgkstNA-6DGK027GYT-M4TXrFGDEWNEcg,405
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=r-Z9DOuHlC36J773x9cBOhBbH_A7gaXFGsjsKZ0aasA,13931
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=_49chh6jo0ikFPVHLfsmV-qROyvyRavkwhF35vV0mVE,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=6XDCkw-1Ku2q4IJGTll32XXOg4pHnfZ3jwRwdXTZRqU,9771
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_3p_del.csv,sha256=P0iNxvqMk9z8jTIYcGjxfKa-T2JIi3eOSh3eXPEnBvM,318
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_5p_del.csv,sha256=G4CoyPjc1MSkQnVijOv2ysz56zGYG4i-QYelQU-un10,635
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/dj_insertion.csv,sha256=kLzxSn3wfZysDk4IhTlgvEsvdNbLWYOJgMTz_nqRJHU,233
@@ -1250,7 +1250,7 @@ test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igh.yaml,sha256=9Pxnw0p8Ug9ZMVcg7X7RMHURhxpWtpj4h93WuuVS-NY,31446
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml,sha256=ZPuU2MYn7BLZmOJ6jUiH-oCa3SaZAr0jVMEAePScKxA,14687
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml,sha256=Ls3u67M8CfP5yaBnfud78p7L9uwH1B0BXGkFwHf48to,6542
-test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=-GlAOXlw3dnaFoGIvNCTqZUtOwfuohwgZainl_kVELk,30344
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=pl0MGy82jrGCT_j1vvoU_tfTplrO1unFUCJdd3R1_Gg,30272
 test/paired/new-results/subset-partition-new-simu/partition-igh.yaml,sha256=HgoqpG1_ChEuLNouoAGTWOJTKXDR9TP6y_TFxIMmprI,66188
 test/paired/new-results/subset-partition-new-simu/partition-igk.yaml,sha256=Mwg9UfLe-e0sYsvxNgiepogOj0DxuIUECIktiMu_f-A,46690
 test/paired/new-results/subset-partition-new-simu/partition-igl.yaml,sha256=Wi-WCJfj2dWt0E0eSbKaSnY9zajo9lzpZnIVw7mF9OY,19395
@@ -1274,7 +1274,7 @@ test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml,sha256=ZUaFW7
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igh.yaml,sha256=AcC85PCqK8Epm4ICu4B8q5eUjtsmlFTQwTkmMhZqQ5I,30562
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igk.yaml,sha256=TrjOFEnyjqRB1mIbZaG2dDUg0BB7h_YMn7P7NJ4siRA,24486
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igl.yaml,sha256=fc2SzIWy51agwAZcCTJZAfZW_-ddT-g0celyJsbelgY,7960
-test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=xBK3OQYUJhd3SKR4WDzBBAgN2eFNAcrECnhcCvKMup4,24838
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=uVpXOtXNSK9BVf4VvAB67mVmOxYsoLjWWwp20SGApq0,24766
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igh.fa,sha256=vR3IfQGVf6SVv6ls-ebrcQmDTDxNu0nhjizzNbitup4,5852
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igk.fa,sha256=_fxa0GOLuWDb0sfWeO4YbSmIcKwuG4F_4fMxte4dYLE,5107
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml,sha256=FjL_OaOcNDHHamp3ehFMyAuU4sO4_TMXgEAPlI1kBdw,22125
@@ -1625,7 +1625,7 @@ test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml,sha256=J_IVfe
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml,sha256=CjHAnWyDZtOL-D2jB_Q0j0om0qtvEhrtZcoOSbk0gSg,45209
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igk.yaml,sha256=93vPGzB3jaCjPPBEUEvqSqf2axzmd1Ry0P6-YoN7OTg,28793
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igl.yaml,sha256=rzwVZ9JijOgNZAWVW5MaiYTNW6HtQvsrqKPV_y9NT30,14925
-test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=ys6d8POjsLaC-Ud2Lmq_KcdtVHAMziwmdxoxw5tJIOA,24786
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=HPZw0OTCC2aGyw7R4WLKfG5YvLLdYizjO43EUMUV8-I,24739
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/igh.fa,sha256=eLpqTnZF03J8ZANDLzei2lXYLU_qMIPYekhVpRgggfk,8772
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/igk.fa,sha256=jWCEqF1B5bXygBLb2BKWKD0rmftFl0c0X5xSEEJOtFA,5868
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml,sha256=mDDRdcCUT4gmdL5IQ1D2nGxXuTxdpEUvt83fNn1K35Q,27612
@@ -1994,7 +1994,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partiti
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igk.yaml,sha256=Ybr2uxzr0wzPyEwrxDWDYif2gFk4UlHNPsXmufeFZhg,50990
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igl/partition-igh.yaml,sha256=2ip81MiUa7l716-y86dipwvwM3qg1VWlRQT-__6o4Rw,29796
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igl/partition-igl.yaml,sha256=dIOx35YYPOx2RQ2e2-Qyac5qegCzHf-DyhML42ZXZIA,21443
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=JqxMSIkznslF8bEDHAZSD0fesdpOup5On-uwPdiDZd8,140730
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=G0YMlBl_kgRFZeJ3NE0JV7cjlOaazzshspd5ZHk0OYA,140753
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/all-mean-mute-freqs.csv,sha256=LPJkL33RJZwT1nbvv80p_1r5J6pSyejnAb1rxjB5eU8,912
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/d_gene-probs.csv,sha256=zeYbss9bxXW-xyVRkX6eBeMhPy-qiino5f0xJ5z86DI,233
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/j_gene-probs.csv,sha256=u4L0N-3x-YChG9C2unXpDbDTVzDZgfw3aChq3fHOuSk,63
@@ -2028,7 +2028,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-33_star_01.yaml,sha256=FU4oDYBlqRgZwlQrbG23AEZneBh-icKPaswTKnXojUI,103996
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-7_star_01.yaml,sha256=GLt0fNZJsArlWs95oE7v2E-ZKciqmRa6plG-AWAxaCg,104240
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV4-39_star_01.yaml,sha256=GGUYeGeP3CaMWhWo4B32FWDF5ohfVAJf8_QwQ9sSkp0,104436
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=4BDj8FBKhoknOr7rqMIFzOY2J6L1JdFBehYd861yy_0,78731
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=nNOGw2WN1HpUN8UfzG2gHDyZ701-vPgonuHSYeZMGVM,78754
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/all-mean-mute-freqs.csv,sha256=yR5AuVGrcUAOe72bT-nEJap_zn3AwCpaXSrFGELbDyA,740
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/d_gene-probs.csv,sha256=p07NACPyIrtcnGVLP8tHoSHCBiO_H7OazG_siOykHws,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/j_gene-probs.csv,sha256=40-_sM8ZQBd6J9r__bewvD1wb3DELCmaRHpLak-xa0s,75
@@ -2047,7 +2047,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV2-30_star_01.yaml,sha256=otPu6N94wuSVkMB8R4ZUYp0k0NLTXBreU1OCCc1VYBk,107159
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-11_star_01.yaml,sha256=dizIw0o2xB1DiUzb_HneMaz3yIIyxS0d2HiPCdwo2fA,102590
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-15_star_01.yaml,sha256=1z0A-rW4uPkaZ0u-3Vu9fxdBoNqsf8MXfaT6yjkaKxw,103093
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=AT9LpUHgCvkPUAfq5DgoevysbLzEI6ndoUjYWcEtFkM,44416
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=S9Nob7g6UxMMfQegxHar8SRWMeZQjFJonPDUpecvg2A,44439
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/all-mean-mute-freqs.csv,sha256=mhl_3xQduo9KwGA20exKyZmQOOdXC5k5HnFS05ySwb0,693
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/d_gene-probs.csv,sha256=fJ9zLdtkRjPmYgE7qmoz00lDMlBYXZIvOc-N_WNztlE,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/j_gene-probs.csv,sha256=ng_-k77f0BCTsX-VM_EGVf0CIxPYj59BGGkibFelC60,39
@@ -8417,8 +8417,8 @@ test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV4-NL1_star_01.csv
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-10-1_star_01.csv,sha256=S075HCAZnbZpAMsXeLMmMXEGVHFs_Euk1XujtFQ46y4,41974
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=QJGyDRqD2JezXsuMbNNXGSCM-kjaN2h4QGpgsaqTqXQ,57817
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV7-4-1_star_02.csv,sha256=k5KeCR5Qa6iEF0IEHR63DDdJStqAjcZxgZOUbKDFNaY,39977
-partis_bcr-1.0.12.dist-info/METADATA,sha256=3SDt4TXOVYyoZ-i6O20NxsmLxdWVxzbmc4wfcXSfU0M,5008
-partis_bcr-1.0.12.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
-partis_bcr-1.0.12.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.12.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.12.dist-info/RECORD,,
+partis_bcr-1.0.12.post1.dev1.dist-info/METADATA,sha256=JYU6Fwkqn8OYJSp80Fq6ML7ZdYIwgmnTRPiM5MJRUmQ,5019
+partis_bcr-1.0.12.post1.dev1.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
+partis_bcr-1.0.12.post1.dev1.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.12.post1.dev1.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.12.post1.dev1.dist-info/RECORD,,

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

@@ -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 = -518.489 NNIs 0 max delta 0.00 Time 0.00
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -518.489 NNIs 0 max delta 0.00 Time 0.00 (final)
-Optimize all lengths: LogLk = -518.489 Time 0.00
+ML-NNI round 3: LogLk = -518.489 NNIs 0 max delta 0.00 Time 0.01 (final)
+Optimize all lengths: LogLk = -518.489 Time 0.01
 Total time: 0.01 seconds Unique: 3/8 Bad splits: 0/0

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

@@ -15,8 +15,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.636 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 = -662.208 NNIs 2 max delta 0.00 Time 0.02
+ML-NNI round 2: LogLk = -662.208 NNIs 2 max delta 0.00 Time 0.04
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -662.208 NNIs 0 max delta 0.00 Time 0.03 (final)
-Optimize all lengths: LogLk = -662.208 Time 0.03
-Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -662.208 NNIs 0 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -662.208 Time 0.04
+Total time: 0.06 seconds Unique: 8/8 Bad splits: 0/5

test/new-results/run-times.csv

@@ -1,9 +1,9 @@
 name,seconds
-cache-parameters-simu,9.0
-annotate-new-simu,3.3
-multi-annotate-new-simu,3.5
-partition-new-simu,7.6
-seed-partition-new-simu,5.2
-vsearch-partition-new-simu,3.5
-get-selection-metrics-new-simu,2.5
-cache-parameters-data,14.5
+cache-parameters-simu,14.4
+annotate-new-simu,4.8
+multi-annotate-new-simu,4.8
+partition-new-simu,8.6
+seed-partition-new-simu,4.8
+vsearch-partition-new-simu,4.7
+get-selection-metrics-new-simu,3.3
+cache-parameters-data,16.6

test/new-results/test.log

@@ -1,16 +1,16 @@
 cache-parameters-simu            partis cache-parameters --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 --is-simu --random-seed 1 --n-procs 10
 caching 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
     keeping 7 / 198 v genes
     missing 8 simulation genes (counts): hv1-202 0  hv2-502 0  hv2-70D04 0  hv3-1104 0  hv3-69-102 0  hv3-902 0  hv4-3401 0  hv4-3909 0
 smith-waterman  (new-allele fitting)
-  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
   removing old sw cache test/new-results/test/parameters/simu/sw-cache.yaml
     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
-    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 7 v genes in 0.1 sec
     running 10 procs for 36 seqs
@@ -18,24 +18,24 @@ smith-waterman  (writing parameters)
       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 (1.1 sec)
-    water time: 1.5  (ig-sw 1.2  processing 0.1)
+    writing parameters to test/new-results/test/parameters/simu/sw (1.9 sec)
+    water time: 2.4  (ig-sw 2.0  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)
+(0.9 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 (1.1 sec)
-    writing parameters to test/new-results/test/parameters/simu/true (1.0 sec)
-         infra time: 2.3
-      hmm step time: 2.9
+    writing parameters to test/new-results/test/parameters/simu/hmm (1.9 sec)
+    writing parameters to test/new-results/test/parameters/simu/true (1.5 sec)
+         infra time: 3.6
+      hmm step time: 4.9
   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
-(0.6 sec)
-      total time: 6.5
+(1.2 sec)
+      total time: 10.4
 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
@@ -46,20 +46,20 @@ 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: 0.1
+        water time: 0.2
 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: 0.8
-      total time: 1.0
+         infra time: 0.2
+      hmm step time: 1.2
+      total time: 1.6
 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])
@@ -67,17 +67,17 @@ 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: 0.1
+        water time: 0.2
 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:  (0.5s) (0.3s)   plotting performance 
+  subcluster annotating 11 clusters with steps:  (0.6s) (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 0.8
-      total time: 1.1
+    subcluster annotation time 1.0
+      total time: 1.4
 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
@@ -88,34 +88,34 @@ 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: 0.1
+        water time: 0.2
 hmm
   --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
   caching all 36 naive sequences (0.9s)
     collapsed 36 queries into 12 clusters with identical naive seqs (0.0 sec)
-  12 clusters with 10 procs (0.3s)
+  12 clusters with 10 procs (0.4s)
    12 clusters with 7 procs (0.3s)
-   12 clusters with 5 procs (0.3s)
-   12 clusters with 3 procs (0.5s)
-   12 clusters with 2 procs (0.4s)
+   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 (0.8s)
-       partition loop time: 2.6
+       partition loop time: 2.2
 getting annotations for final partition
-  subcluster annotating 10 clusters with steps:  (0.5s) (0.3s) (0.4s)   plotting performance 
+  subcluster annotating 10 clusters with steps:  (0.7s) (0.3s) (0.2s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: d8761c689a
-(0.1 sec)
+(0.0 sec)
 
-    subcluster annotation time 1.3
-      total time: 5.2
+    subcluster annotation time 1.2
+      total time: 4.7
 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 0.3 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
       removed 25 / 36 = 0.69 sequences with cdr3 length different from seed sequence (leaving 11)
-        water time: 0.1
+        water time: 0.0
 hmm
   --persistent-cachefname: using existing hmm cache file test/new-results/cache-new-partition.csv
    collapsed 11 queries into 2 clusters with identical naive seqs (0.0 sec)
@@ -124,12 +124,12 @@ hmm
        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: 0.5
+       partition loop time: 0.3
 getting annotations for final partition
-  subcluster annotating 1 cluster with steps:  (0.4s) (0.3s) (0.2s) 
+  subcluster annotating 1 cluster with steps:  (0.3s) (0.3s) (0.3s) 
     subcluster annotation time 0.9
   seed cluster size in best partition: 11, excluding seed seq: 10
-      total time: 1.9
+      total time: 1.5
 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
@@ -146,9 +146,9 @@ hmm
       vsearch time: 0.4
 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:  (0.4s) (0.2s) (0.2s) 
-    subcluster annotation time 0.8
-      total time: 1.5
+  subcluster annotating 10 clusters with steps:  (0.7s) (0.3s) (0.2s) 
+    subcluster annotation time 1.2
+      total time: 1.8
 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).
@@ -172,13 +172,13 @@ 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: 0.5
+      total time: 0.6
 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
   --input-metafnames: added meta info for 4 sequences from test/input-meta.yaml: multiplicities
 caching parameters
-  vsearch: 44 / 50 v annotations (6 failed) with 54 v genes in 0.1 sec
+  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 0.1 sec
@@ -186,28 +186,28 @@ smith-waterman  (new-allele fitting)
     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 0.1)
+    water time: 0.5  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.1 sec
+  vsearch: 45 / 50 v annotations (5 failed) with 23 v genes in 0.2 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 (2.4 sec)
-    water time: 2.9  (ig-sw 2.5  processing 0.1)
+    writing parameters to test/new-results/test/parameters/data/sw (2.1 sec)
+    water time: 2.6  (ig-sw 2.2  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
-(2.6 sec)
+(2.3 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 (1.2 sec)
-         infra time: 1.4
-      hmm step time: 3.6
+    writing parameters to test/new-results/test/parameters/data/hmm (2.5 sec)
+         infra time: 2.7
+      hmm step time: 5.0
   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
-(1.9 sec)
-      total time: 11.8
+(2.0 sec)
+      total time: 13.0

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

@@ -9,7 +9,7 @@ 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
-ML-NNI round 1: LogLk = -1718.230 NNIs 0 max delta 0.00 Time 0.02
+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
 Switched to using 20 rate categories (CAT approximation)
@@ -19,5 +19,5 @@ Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -1660.926 NNIs 0 max delta 0.00 Time 0.05
 Turning off heuristics for final round of ML NNIs (converged)
 ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.06 (final)
-Optimize all lengths: LogLk = -1660.925 Time 0.07
-Total time: 0.09 seconds Unique: 8/8 Bad splits: 0/5
+Optimize all lengths: LogLk = -1660.925 Time 0.06
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

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

@@ -9,7 +9,7 @@ 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
-ML-NNI round 1: LogLk = -1516.977 NNIs 0 max delta 0.00 Time 0.02
+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
 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 = -1478.012 NNIs 0 max delta 0.00 Time 0.05
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.07 (final)
-Optimize all lengths: LogLk = -1478.012 Time 0.07
-Total time: 0.09 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.06 (final)
+Optimize all lengths: LogLk = -1478.012 Time 0.06
+Total time: 0.08 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 0.04
+ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03
 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 0.05
+Optimize all lengths: LogLk = -1274.638 Time 0.04
 Total time: 0.06 seconds Unique: 6/6 Bad splits: 0/3

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

@@ -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 = -968.458 NNIs 0 max delta 0.00 Time 0.03
 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 0.03
-Total time: 0.04 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.04 (final)
+Optimize all lengths: LogLk = -968.417 Time 0.04
+Total time: 0.05 seconds Unique: 8/8 Bad splits: 0/5

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

@@ -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 0.02 (final)
-Optimize all lengths: LogLk = -794.321 Time 0.02
-Total time: 0.03 seconds Unique: 7/7 Bad splits: 0/4
+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