partis-bcr 1.0.12.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl → 1.0.13__cp312-cp312-macosx_10_13_universal2.whl

{partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.12.post1.dev3
+Version: 1.0.13
 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.post1.dev3.dist-info → partis_bcr-1.0.13.dist-info}/RECORD

@@ -303,18 +303,30 @@ data/substitution-profiles/GSSPs_for_VK_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha256=CMFb1gk8MbfaMb6y0_qLLiKErrx866C2EafKRSPesB4,184979
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
 packages/bpp/bin/bppseqgen,sha256=miMtwBdGjJLBV0d40VfLzqy9X2P9d6xNqFxFopRkepY,202788
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 packages/ham/bcrham,sha256=3kZbsUpwEPzVy5v1X7HH3o_0HbX5vmV-w17opGl1-wk,768288
 packages/ig-sw/src/ig_align/ig-sw,sha256=Pl5ghiN_OYvM3299ErtwOYPhoWECl3fyzIHWAKPtTKE,387408
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 python/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 python/alleleclusterer.py,sha256=x50E_lJMlKPc-CPkdkM1qe4AvVi-mkDJ1cBDxs5L-ms,30551
 python/allelefinder.py,sha256=SgJjopk5ivLOcmTumsWq5PZ05aPZ6zQyjTd1fxeRjaM,80402
@@ -380,9 +392,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
 test/new-results/get-selection-metrics-new-simu.yaml,sha256=Rhg9agnpuFIQfNs6LUhUrxJBM1WwwHMPkxYGAVQKjSE,8793
 test/new-results/multi-annotate-new-simu.yaml,sha256=dBpOYLfvkma-Tfy-DNAxsf7zB8niCRbuFSEbvSvsDLE,37319
 test/new-results/partition-new-simu.yaml,sha256=oQ1MSYpR_1ArYPfoLGYFBwaNDOrCcQ9IY0Rij75CJD8,37726
-test/new-results/run-times.csv,sha256=MXJFOLNb92f4hIOwB8nMj886QFrAeqvpp_xO65nBQ2k,241
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 test/new-results/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=4m0lUpFm49ErSqRDDmMQ3outlXceIGI81hLTp5QghbY,16441
+test/new-results/test.log,sha256=o5yexPdhCbQkhmB7mMqdcOxdmWcXDeIEB3rjsASnl68,16442
 test/new-results/vsearch-partition-new-simu.yaml,sha256=8TCi7_M9ozjXkK82q2vdMD4yUgxwmjjORXPJVmrgReY,36290
 test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv,sha256=ybPnGto_Ly4XhxcAaF48lH-eTqnlFi7GDvJ4f9dXP9Y,153
 test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv,sha256=G1sT72mKm3q7QcXXDsDGdwbD-arhzQBV5k7id54LB_g,166
@@ -504,13 +516,13 @@ test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_ha
 test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
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 test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=qokRcGSD1p1XlPUBpYFMm8HYpMKfb4ed4d5PwKMVC6E,4377
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 test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=PbcyyZtEcJqvPm8PLFeZDbICNpKJxJCMyfhdV3-dY_I,3061
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 test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=hMJ15y6H0hZmELwThgvWl2Vpb2FkzIxwk7667oSuscc,279
 test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa,sha256=UdE9X7VYtEqKx8zo0lP2gQh9mTnpsrT_R8p0jkS_wgs,3133
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 test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv,sha256=ybPnGto_Ly4XhxcAaF48lH-eTqnlFi7GDvJ4f9dXP9Y,153
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 test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv,sha256=1uCusAdxgbGGytCri7146q90JBg6SQ2Od8Gfkj4TCp8,194
@@ -975,8 +987,8 @@ test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv,sha256
 test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-61_star_01.csv,sha256=kONUU7EHhpBiHqSGDoWdTA5zBjaMYZDo385OHxsD5_w,40111
 test/new-results/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=0BOZU7pYns4oh593bGeq2V-qPaLAdH33RodQUnwDmlo,38980
 test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=1OOMLjMahLNNNKO_5-S9SnpiH4ep2t_SkGWMIr3yHVY,12599
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-test/paired/new-results/test.log,sha256=vIqmwSnQlFOjz5Bw2U7qEXOb4sxzrTx053MpMmHZlVs,72233
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 test/paired/new-results/partition-new-simu/partition-igh.yaml,sha256=qelM_0rtDDwpLWl6_ItvkrXioZ9MI6VMiLPMf6tcbIs,71140
 test/paired/new-results/partition-new-simu/partition-igk.yaml,sha256=9iTcIjgyiVsoADqym9El14fwDT4nU_xu2mWy_UeVHSA,46688
 test/paired/new-results/partition-new-simu/partition-igl.yaml,sha256=XdV7rr3fQJPi3-5NvCxhHI4k5huOja8zxdI9XHWatMQ,23871
@@ -991,39 +1003,39 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
 test/paired/new-results/partition-new-simu/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
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 test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml,sha256=o-a0agImpMjjo32u7TaIrHbTW_RXJPkHXD8znweeT8Y,38067
 test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml,sha256=vEjx11N8dkIpx00_h5_qM4dis3254HeEsza7qkTre4I,18883
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/func-per-drop.csv,sha256=hcFbqQj-_5cXQ7nwQk60LucTJs4Sjwctn8UhwGMrvjk,305
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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
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 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
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 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
@@ -1251,7 +1263,7 @@ 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=JvkQMoHdxa0ueQ95nMcyJY-GUz5wumNZ4xltn4_-k3E,30272
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 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
@@ -1275,7 +1287,7 @@ 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=-EnCee3Y1Y5K_oHOwmJBY3fvyRulV3BODkrhp7gJe7E,24766
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 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
@@ -1626,7 +1638,7 @@ 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=VsUPc_1ZXDLMBMse4Pit9hnOE1wMWpYDyG_r_9PI8N8,24714
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 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
@@ -1995,7 +2007,7 @@ 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=Db_QZH8sHfUS54VNMKl6te_5myvzVeY7Bd52VCh9EhI,140753
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 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
@@ -2029,7 +2041,7 @@ 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=MJTPUkvAD5zSzp5NVJlndgIuVkQ4fyp5DmIbi_wCWDQ,78754
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 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
@@ -2048,7 +2060,7 @@ 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=MZhvAmjeoRC_uSdYmn5h0JluXlTyiBxTca6xASMMlfg,44439
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 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
@@ -8418,8 +8430,8 @@ 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.post1.dev3.dist-info/METADATA,sha256=xtJwjJ-RYD8RZonfoC-QHhGkgVXfd4HNUv0qe75k-8Y,5019
-partis_bcr-1.0.12.post1.dev3.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
-partis_bcr-1.0.12.post1.dev3.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.12.post1.dev3.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.12.post1.dev3.dist-info/RECORD,,
+partis_bcr-1.0.13.dist-info/METADATA,sha256=pxYl-D456L0qwiG6VKINxSsnHB0JVUCTUd4_sloWXrg,5008
+partis_bcr-1.0.13.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
+partis_bcr-1.0.13.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.13.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.13.dist-info/RECORD,,

test/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 48 times)
 Initial topology in 0.00 seconds
 Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
-Total branch-length 0.082 after 0.00 sec
+Total branch-length 0.082 after 0.01 sec
 ML-NNI round 1: LogLk = -667.315 NNIs 1 max delta 0.00 Time 0.01
 GTR Frequencies: 0.2215 0.2569 0.3074 0.2143
 GTR rates(ac ag at cg ct gt) 0.9744 0.9603 0.4580 0.6925 0.8029 1.0000
@@ -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 = -654.776 NNIs 1 max delta 0.00 Time 0.02
+ML-NNI round 2: LogLk = -654.776 NNIs 1 max delta 0.00 Time 0.05
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -654.776 NNIs 0 max delta 0.00 Time 0.02 (final)
-Optimize all lengths: LogLk = -654.776 Time 0.02
-Total time: 0.03 seconds Unique: 8/12 Bad splits: 0/5
+ML-NNI round 3: LogLk = -654.776 NNIs 0 max delta 0.00 Time 0.05 (final)
+Optimize all lengths: LogLk = -654.776 Time 0.06
+Total time: 0.08 seconds Unique: 8/12 Bad splits: 0/5

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

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.624 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 = -518.489 NNIs 0 max delta 0.00 Time 0.00
+ML-NNI round 2: LogLk = -518.489 NNIs 0 max delta 0.00 Time 0.01
 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 0.05
 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 0.06 (final)
+Optimize all lengths: LogLk = -662.208 Time 0.06
+Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5

test/new-results/run-times.csv

@@ -1,9 +1,9 @@
 name,seconds
-cache-parameters-simu,7.7
-annotate-new-simu,2.8
-multi-annotate-new-simu,2.7
-partition-new-simu,5.7
-seed-partition-new-simu,2.9
-vsearch-partition-new-simu,3.3
-get-selection-metrics-new-simu,2.3
-cache-parameters-data,9.5
+cache-parameters-simu,9.9
+annotate-new-simu,3.9
+multi-annotate-new-simu,4.6
+partition-new-simu,8.1
+seed-partition-new-simu,4.4
+vsearch-partition-new-simu,4.3
+get-selection-metrics-new-simu,4.2
+cache-parameters-data,14.9