partis-bcr 1.0.9.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl → 1.0.9.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl

{partis_bcr-1.0.9.post1.dev3.dist-info → partis_bcr-1.0.9.post1.dev4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.9.post1.dev3
+Version: 1.0.9.post1.dev4
 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-1.0.9.post1.dev3.dist-info → partis_bcr-1.0.9.post1.dev4.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
 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
@@ -373,7 +373,7 @@ test/phylo-naive-run.py,sha256=pTyXPv0CBddu0CVPetORRazoYyKzYa427Cwtpcuq7DE,5282
 test/run-gl-inference.sh,sha256=XK3cs5xQad5LAoVaVp2-3IMJssml8ZBNYPwLRrlW2vg,1408
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 test/test.py,sha256=CS0H2eckShv9TIPh-p_6jeaBuDd3zlRTDjaHmXU3Ln4,63749
-test/new-results/test.log,sha256=GyE9k-0FmvgwRUbLItZveGCBOFJP9DtWP1Wd9rtqu2I,1858
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 test/new-results/test/parameters/simu/sw-cache.yaml,sha256=xRR9tZOPBIIU2d3QmiWCUcprRlXZre8BhmMONmgAcq8,24635
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 test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv,sha256=8n9PeG1kl44R8PSBy80bm-EXIUbUR2Oae53USbydt9o,2435
@@ -456,8 +456,8 @@ test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ6_star_02.csv,sha256=-nv
 test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv,sha256=L2u0w3IWDJKOshqCT6St6SxKKPAjq6JbY0JDH9uBMls,39711
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-test/paired/new-results/test.log,sha256=Ee5xgVs5OhcMJTgdqzLcmIVVuf0euzw_aP7uKKTAoVQ,72235
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 test/paired/new-results/partition-new-simu/partition-igh.yaml,sha256=qelM_0rtDDwpLWl6_ItvkrXioZ9MI6VMiLPMf6tcbIs,71140
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 test/paired/new-results/partition-new-simu/partition-igl.yaml,sha256=XdV7rr3fQJPi3-5NvCxhHI4k5huOja8zxdI9XHWatMQ,23871
@@ -472,13 +472,13 @@ 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/fasttree/iclust-0/input-seqs.fa,sha256=uHZPu9HHvPAYd4yBC8o-FOdG0jH4ACJcCMhA4dmvvlY,5918
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 test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml,sha256=TvdmgfDmKq9FTXSZ8WvsP85OsORW3qB2hqMbGZG7_Ss,43157
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml,sha256=nnmC59opTanhhUFLO4Nz8BeKZvZ0QBr-oblRejb8eUo,4667
@@ -488,10 +488,10 @@ test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust
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 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out,sha256=Qy5GcANnwMQQ3RMail9Te4CcLtZm-QcECudLEMDlv3w,261
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@@ -501,7 +501,7 @@ test/paired/new-results/partition-new-simu/igh+igl/partition-igl-selection-metri
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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
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=AqKu2TVGrgsXy6aYWFmyEKsXBrSa4MG47RU17Mr0qV0,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=wPsYK2wCbB18kWKeS7cMLeGW8iZn7Uk7kuYB4-pLlLc,7249
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=3x7eYQ6BmQLBinN65scJrt2gBk51yptYOJ4YP9tHl_Q,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=oxVbABqG1xvRtuk9ZxxAJ3sjwPgING_OK4B6AuZScZA,7249
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.csv,sha256=6H8vsJkv89E5OaepY5bg1DnptEIePK6-C6QjuaBRXv4,337
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=MjtNphTAULScVU7oXYUeqwoa3pAMneMMPkFLvZxvoi4,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=hVhB7UEPHeihqQGAKh7BOoi2sxRx74LA9CtNiSuda_Q,13482
 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=oC2LY7gekuVp1je7zE5pV5ZNXlUoo04iBowg0sV6Zuk,13931
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=mF-A6529BptIECOyXWnZ8VqRxPKeiCrxy1gV4xmwzh0,13931
 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=FARYVQNiG4QM6065Ru7xj24gsPyCsxHq9JYa27IghUs,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=FgS10tsvzlJpoczqawOg6jJNpH3RBXYnstB1QAGVd7g,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
@@ -732,7 +732,7 @@ 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=R1iHD4ABM77sI9epqumnkTEhCLuBA0QiP7liNgGtajg,30272
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=05IpG8CQTti40RLhYacq8RPGhFcpIM0uS3RkDIAYzsI,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
@@ -756,7 +756,7 @@ 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=sRGZxfrpTRLnWq7-6PSiR2k4Uwlbfjk3Og1nojwg59o,24766
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=Ps8U8bko5WXjKp6MRS2C4g0whyH3b53gTqDol4eQ_F4,24766
 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
@@ -1107,7 +1107,7 @@ 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=i3JBt7YtwCfxf67B459SSVsNq1zna6DRih9RxixAAd8,24739
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=BNcfGrTAZ-_jmzoFQb3wUtvr1x2OhrtDHqnzxfQBKlQ,24714
 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
@@ -1476,7 +1476,7 @@ 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=S9Uy5hGmnuT74GNsbcImB8-V44vKwDWwGyTjHCTfjCg,140752
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=QUX0wP55sktXMX49gqcqEenAun7z4stCXgzA5o71mpA,140752
 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
@@ -1510,7 +1510,7 @@ 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=FA1BJpgH3WLhOIKOeaLS8rYgNlMgHWp0UOoUEfO9C78,78753
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=Do_FgxH-dyILHe0BBtF3YETnlvlsqj93R7QLXol6bhg,78753
 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
@@ -1529,7 +1529,7 @@ 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=VZJn7d6YXos-xbHXvqMLwaXse2KaB0a1245Qg3LgZAo,44438
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=isNJ1pgviC7y9N9BxBwhFiflk3Sa6oQAvtZO-RlSd70,44438
 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
@@ -7899,8 +7899,8 @@ 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-1.0.9.post1.dev3.dist-info/METADATA,sha256=WIWPgmaUIKJnLFWBip7OJ9uwXZUv8pLkGj6rYgKbcG8,5018
-partis_bcr-1.0.9.post1.dev3.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
-partis_bcr-1.0.9.post1.dev3.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.9.post1.dev3.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.9.post1.dev3.dist-info/RECORD,,
+partis_bcr-1.0.9.post1.dev4.dist-info/METADATA,sha256=It1oogNI2l0nqI-cn-ab79H0mt5TC6hmsJLZNdtrMgE,5018
+partis_bcr-1.0.9.post1.dev4.dist-info/WHEEL,sha256=_N1vyLgwJ10g4JxFsp-IfU42zGJgf-DUqwfdbV1YvEM,115
+partis_bcr-1.0.9.post1.dev4.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.9.post1.dev4.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.9.post1.dev4.dist-info/RECORD,,

test/new-results/test.log

@@ -4,7 +4,7 @@ caching parameters
   vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.2 sec
     keeping 2 / 198 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.2 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 2 v genes in 0.1 sec
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 10 (1.000) unproductive
@@ -15,20 +15,20 @@ smith-waterman  (writing parameters)
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 10 (1.000) unproductive
         writing sw results to test/new-results/test/parameters/simu/sw-cache.yaml
-    writing parameters to test/new-results/test/parameters/simu/sw (5.4 sec)
-    water time: 5.6  (ig-sw 5.5  processing 0.2)
+    writing parameters to test/new-results/test/parameters/simu/sw (8.1 sec)
+    water time: 8.3  (ig-sw 8.2  processing 0.1)
   writing hmms     removed 35 genes from glfo (leaving v 2  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.4 sec)
+(0.2 sec)
 hmm
     reading output
         read 10 hmm output lines with 10 sequences in 10 events  (0 failures)
-    writing parameters to test/new-results/test/parameters/simu/hmm (0.5 sec)
-         infra time: 0.6
-      hmm step time: 1.0
+    writing parameters to test/new-results/test/parameters/simu/hmm (0.3 sec)
+         infra time: 0.4
+      hmm step time: 0.7
   writing hmms     removed 0  genes from glfo (leaving v 2  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: 8.1
+      total time: 10.3

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

@@ -9,16 +9,15 @@ 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 0.05
+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)
 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 0.10
+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)
-      0.10 seconds: ML NNI round 3 of 6, 1 of 6 splits
-ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.12 (final)
-Optimize all lengths: LogLk = -1660.925 Time 0.12
-Total time: 0.14 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.05 (final)
+Optimize all lengths: LogLk = -1660.925 Time 0.06
+Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5

test/paired/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 0.652 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 0.05
+ML-NNI round 2: LogLk = -1478.012 NNIs 0 max delta 0.00 Time 0.04
 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
+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 0.04
+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 0.05 (final)
-Optimize all lengths: LogLk = -1274.638 Time 0.06
-Total time: 0.08 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 0.04
+Total time: 0.05 seconds Unique: 6/6 Bad splits: 0/3

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

@@ -19,5 +19,5 @@ 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 0.03
+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

@@ -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 = -457.145 NNIs 0 max delta 0.00 Time 0.01
+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 0.01 (final)
-Optimize all lengths: LogLk = -457.145 Time 0.01
+ML-NNI round 3: LogLk = -457.145 NNIs 0 max delta 0.00 Time 0.00 (final)
+Optimize all lengths: LogLk = -457.145 Time 0.00
 Total time: 0.01 seconds Unique: 3/8 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 0.03 (final)
-Optimize all lengths: LogLk = -1077.702 Time 0.04
-Total time: 0.05 seconds Unique: 9/9 Bad splits: 0/6
+Optimize all lengths: LogLk = -1077.702 Time 0.03
+Total time: 0.04 seconds Unique: 9/9 Bad splits: 0/6