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Refactor csubst runtime and output handling
1 parent 4562063 commit 24d6c51

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-11854
lines changed

‎AGENTS.md‎

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This file was deleted.

‎csubst/csubst‎

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‎csubst/dataset/PGK.alignment.fa.iqtree‎

Lines changed: 37 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ IQ-TREE 2.3.6 built Aug 4 2024
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Input file name: /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa
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User tree file name: tmp.csubst.nwk
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Type of analysis: tree reconstruction
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Random seed number: 765051
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Random seed number: 693358
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REFERENCES
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----------
@@ -28,46 +28,47 @@ Number of distinct site patterns: 405
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SUBSTITUTION PROCESS
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--------------------
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31-
Model of substitution: GY+F3X4+R4
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33-
State frequencies:
34-
pi(AAA) = 0.0171 pi(AAC) = 0.0287 pi(AAG) = 0.0278 pi(AAT) = 0.0273
35-
pi(ACA) = 0.0114 pi(ACC) = 0.0192 pi(ACG) = 0.0186 pi(ACT) = 0.0182
36-
pi(AGA) = 0.0093 pi(AGC) = 0.0156 pi(AGG) = 0.0150 pi(AGT) = 0.0148
37-
pi(ATA) = 0.0164 pi(ATC) = 0.0276 pi(ATG) = 0.0267 pi(ATT) = 0.0262
38-
pi(CAA) = 0.0085 pi(CAC) = 0.0143 pi(CAG) = 0.0139 pi(CAT) = 0.0136
39-
pi(CCA) = 0.0057 pi(CCC) = 0.0096 pi(CCG) = 0.0093 pi(CCT) = 0.0091
40-
pi(CGA) = 0.0046 pi(CGC) = 0.0078 pi(CGG) = 0.0075 pi(CGT) = 0.0074
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pi(CTA) = 0.0082 pi(CTC) = 0.0138 pi(CTG) = 0.0133 pi(CTT) = 0.0131
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pi(GAA) = 0.0220 pi(GAC) = 0.0370 pi(GAG) = 0.0357 pi(GAT) = 0.0351
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pi(GCA) = 0.0147 pi(GCC) = 0.0247 pi(GCG) = 0.0239 pi(GCT) = 0.0235
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pi(GGA) = 0.0119 pi(GGC) = 0.0200 pi(GGG) = 0.0193 pi(GGT) = 0.0190
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pi(GTA) = 0.0211 pi(GTC) = 0.0356 pi(GTG) = 0.0344 pi(GTT) = 0.0338
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pi(TAC) = 0.0118 pi(TAT) = 0.0112 pi(TCA) = 0.0047 pi(TCC) = 0.0079
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pi(TCG) = 0.0076 pi(TCT) = 0.0075 pi(TGC) = 0.0064 pi(TGG) = 0.0062
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pi(TGT) = 0.0060 pi(TTA) = 0.0067 pi(TTC) = 0.0113 pi(TTG) = 0.0109
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pi(TTT) = 0.0107
31+
Model of substitution: ECMK07+F+R4
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33+
State frequencies: (empirical counts from alignment)
34+
35+
pi(AAA) = 0.0411 pi(AAC) = 0.0295 pi(AAG) = 0.0590 pi(AAT) = 0.0219
36+
pi(ACA) = 0.0049 pi(ACC) = 0.0138 pi(ACG) = 0.0032 pi(ACT) = 0.0188
37+
pi(AGA) = 0.0058 pi(AGC) = 0.0166 pi(AGG) = 0.0055 pi(AGT) = 0.0073
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pi(ATA) = 0.0073 pi(ATC) = 0.0268 pi(ATG) = 0.0351 pi(ATT) = 0.0163
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pi(CAA) = 0.0059 pi(CAC) = 0.0077 pi(CAG) = 0.0114 pi(CAT) = 0.0070
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pi(CCA) = 0.0129 pi(CCC) = 0.0073 pi(CCG) = 0.0019 pi(CCT) = 0.0185
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pi(CGA) = 0.0041 pi(CGC) = 0.0025 pi(CGG) = 0.0055 pi(CGT) = 0.0010
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pi(CTA) = 0.0065 pi(CTC) = 0.0148 pi(CTG) = 0.0364 pi(CTT) = 0.0127
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pi(GAA) = 0.0232 pi(GAC) = 0.0317 pi(GAG) = 0.0394 pi(GAT) = 0.0269
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pi(GCA) = 0.0116 pi(GCC) = 0.0404 pi(GCG) = 0.0036 pi(GCT) = 0.0406
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pi(GGA) = 0.0268 pi(GGC) = 0.0245 pi(GGG) = 0.0156 pi(GGT) = 0.0284
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pi(GTA) = 0.0109 pi(GTC) = 0.0252 pi(GTG) = 0.0325 pi(GTT) = 0.0215
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pi(TAC) = 0.0057 pi(TAT) = 0.0049 pi(TCA) = 0.0038 pi(TCC) = 0.0137
48+
pi(TCG) = 0.0013 pi(TCT) = 0.0143 pi(TGC) = 0.0076 pi(TGG) = 0.0098
49+
pi(TGT) = 0.0097 pi(TTA) = 0.0044 pi(TTC) = 0.0171 pi(TTG) = 0.0151
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pi(TTT) = 0.0204
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Model of rate heterogeneity: FreeRate with 4 categories
51-
Site proportion and rates: (0.0070,0.3202) (0.0241,0.3358) (0.5230,0.6146) (0.4458,1.4988)
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Site proportion and rates: (0.0091,0.2650) (0.0315,0.3789) (0.7594,0.8278) (0.2000,1.7853)
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Category Relative_rate Proportion
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1 0.3202 0.0070
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2 0.3358 0.0241
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3 0.6146 0.5230
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4 1.4988 0.4458
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1 0.2650 0.0091
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2 0.3789 0.0315
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3 0.8278 0.7594
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4 1.7853 0.2000
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USER TREE
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---------
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Log-likelihood of the tree: -13212.5631 (s.e. 322.6696)
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Log-likelihood of the tree: -13284.1525 (s.e. 296.1788)
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Unconstrained log-likelihood (without tree): -2487.2259
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Number of free parameters (#branches + #model parameters): 80
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Akaike information criterion (AIC) score: 26585.1262
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Corrected Akaike information criterion (AICc) score: 26623.6976
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Bayesian information criterion (BIC) score: 26907.7731
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Number of free parameters (#branches + #model parameters): 129
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Akaike information criterion (AIC) score: 26826.3050
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Corrected Akaike information criterion (AICc) score: 26943.1691
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Bayesian information criterion (BIC) score: 27346.5731
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Total tree length (sum of branch lengths): 8.9041
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Sum of internal branch lengths: 3.1335 (35.1914% of tree length)
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Total tree length (sum of branch lengths): 7.5701
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Sum of internal branch lengths: 2.6640 (35.1914% of tree length)
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NOTE: Tree is UNROOTED although outgroup taxon 'Anolis_carolinensis_ENSACAG00000003255' is drawn at root
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@@ -142,7 +143,7 @@ NOTE: Branch lengths are interpreted as number of nucleotide substitutions per c
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Tree in newick format:
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(Anolis_carolinensis_ENSACAG00000003255:0.4834024147,((((Astyanax_mexicanus_ENSAMXG00000007127:0.2451158286,Danio_rerio_ENSDARG00000054191:0.3588177795)Node5:0.1443292912,(Gadus_morhua_ENSGMOG00000013283:0.4584374219,(Oreochromis_niloticus_ENSONIG00000017337:0.2616088974,Oryzias_latipes_ENSORLG00000014063:0.2456033069)Node7:0.1338415260)Node6:0.2178495226)Node4:0.3468695281,(((((((((Bos_taurus_ENSBTAG00000000894:0.0168606748,Ovis_aries_ENSOARG00000018803:0.0195228712)Node16:0.0653311811,Sus_scrofa_ENSSSCG00000012440:0.0884976033)Node15:0.0140934806,Canis_lupus_ENSCAFG00000017270:0.1141186295)Node14:0.0321144576,Chinchilla_lanigera_ENSCLAG00000000146:0.1579062592)Node13:0.0042562276,(Oryctolagus_cuniculus_ENSOCUG00000014726:0.0000083203,Oryctolagus_cuniculus_ENSOCUG00000025100:0.1160779609)Node17:0.1235768770)Node12:0.0039485415,(Callithrix_jacchus_ENSCJAG00000021082:0.0496032681,(Homo_sapiens_ENSG00000102144:0.0133653485,Macaca_mulatta_ENSMMUG00000013725:0.0604814057)Node19:0.0096177416)Node18:0.0456475817)Node11:0.0222437534,(Mus_musculus_ENSMUSG00000062070:0.0443650689,Rattus_norvegicus_ENSRNOG00000058249:0.0683706942)Node20:0.1302973219)Node10:0.0916137618,(((Callithrix_jacchus_ENSCJAG00000022394:0.0791130783,(Homo_sapiens_ENSG00000170950:0.0415252888,Macaca_mulatta_ENSMMUG00000011998:0.0425905311)Node24:0.0222364461)Node23:0.0845912818,((Mus_musculus_ENSMUSG00000031233:0.1659046701,Rattus_norvegicus_ENSRNOG00000013600:0.1180002686)Node26:0.3275360296,Oryctolagus_cuniculus_ENSOCUG00000005270:0.2479809407)Node25:0.0243772584)Node22:0.0541588028,(Ovis_aries_ENSOARG00000008736:0.1579916734,Sus_scrofa_ENSSSCG00000001738:0.1960714880)Node27:0.0851966512)Node21:0.2839705420)Node9:0.1261159211,((Monodelphis_domestica_ENSMODG00000004055:0.0310424276,((Monodelphis_domestica_ENSMODG00000022821:0.0058259661,Monodelphis_domestica_ENSMODG00000025017:0.0069887365)Node31:0.0465234837,Monodelphis_domestica_ENSMODG00000023304:0.1511156642)Node30:0.0126563128)Node29:0.2010888442,Monodelphis_domestica_ENSMODG00000023385:0.5783681174)Node28:0.0994205590)Node8:0.1885498380)Node3:0.1003555689,Xenopus_tropicalis_ENSXETG00000007447:0.6916800207)Node2:0.0910616545,Gallus_gallus_ENSGALG00000007936:0.4542543972)Node1;
146+
(Anolis_carolinensis_ENSACAG00000003255:0.4109784078,((((Astyanax_mexicanus_ENSAMXG00000007127:0.2083922419,Danio_rerio_ENSDARG00000054191:0.3050592119)Node5:0.1227056806,(Gadus_morhua_ENSGMOG00000013283:0.3897537041,(Oreochromis_niloticus_ENSONIG00000017337:0.2224142967,Oryzias_latipes_ENSORLG00000014063:0.2088066855)Node7:0.1137892066)Node6:0.1852110110)Node4:0.2949010638,(((((((((Bos_taurus_ENSBTAG00000000894:0.0143345856,Ovis_aries_ENSOARG00000018803:0.0165979281)Node16:0.0555431748,Sus_scrofa_ENSSSCG00000012440:0.0752387720)Node15:0.0119819761,Canis_lupus_ENSCAFG00000017270:0.0970212213)Node14:0.0273030259,Chinchilla_lanigera_ENSCLAG00000000146:0.1342485287)Node13:0.0036185538,(Oryctolagus_cuniculus_ENSOCUG00000014726:0.0000070737,Oryctolagus_cuniculus_ENSOCUG00000025100:0.0986870030)Node17:0.1050624213)Node12:0.0033569656,(Callithrix_jacchus_ENSCJAG00000021082:0.0421716390,(Homo_sapiens_ENSG00000102144:0.0113629338,Macaca_mulatta_ENSMMUG00000013725:0.0514199993)Node19:0.0081767985)Node18:0.0388085990)Node11:0.0189111640,(Mus_musculus_ENSMUSG00000062070:0.0377182340,Rattus_norvegicus_ENSRNOG00000058249:0.0581273038)Node20:0.1107760000)Node10:0.0778880635,(((Callithrix_jacchus_ENSCJAG00000022394:0.0672602494,(Homo_sapiens_ENSG00000170950:0.0353039136,Macaca_mulatta_ENSMMUG00000011998:0.0362095599)Node24:0.0189049515)Node23:0.0719177009,((Mus_musculus_ENSMUSG00000031233:0.1410486068,Rattus_norvegicus_ENSRNOG00000013600:0.1003213079)Node26:0.2784641364,Oryctolagus_cuniculus_ENSOCUG00000005270:0.2108280990)Node25:0.0207250244)Node22:0.0460446574,(Ovis_aries_ENSOARG00000008736:0.1343211461,Sus_scrofa_ENSSSCG00000001738:0.1666957911)Node27:0.0724323731)Node21:0.2414256893)Node9:0.1072210623,((Monodelphis_domestica_ENSMODG00000004055:0.0263916089,((Monodelphis_domestica_ENSMODG00000022821:0.0049531119,Monodelphis_domestica_ENSMODG00000025017:0.0059416745)Node31:0.0395532721,Monodelphis_domestica_ENSMODG00000023304:0.1284753099)Node30:0.0107601268)Node29:0.1709614402,Monodelphis_domestica_ENSMODG00000023385:0.4917162197)Node28:0.0845252357)Node8:0.1603010449)Node3:0.0853201612,Xenopus_tropicalis_ENSXETG00000007447:0.5880515796)Node2:0.0774186736,Gallus_gallus_ENSGALG00000007936:0.3861973858)Node1;
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ALISIM COMMAND
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@@ -153,7 +154,7 @@ For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim
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TIME STAMP
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Date and time: Thu Feb 26 17:29:01 2026
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Total CPU time used: 33.3672 seconds (0h:0m:33s)
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Total wall-clock time used: 34.0662 seconds (0h:0m:34s)
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Date and time: Wed Mar 4 11:11:49 2026
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Total CPU time used: 17.1126 seconds (0h:0m:17s)
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Total wall-clock time used: 17.2697 seconds (0h:0m:17s)
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‎csubst/dataset/PGK.alignment.fa.log‎

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Original file line numberDiff line numberDiff line change
@@ -3,19 +3,19 @@ Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
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Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong
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Host: fukushimakenjis-Mac-Studio.local (SSE4.2, 64 GB RAM)
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Command: iqtree -s /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa -te tmp.csubst.nwk -m GY+F3X4+R4 --seqtype CODON1 --threads-max 1 -T AUTO --ancestral --rate --redo --prefix /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa
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Seed: 765051 (Using SPRNG - Scalable Parallel Random Number Generator)
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Time: Thu Feb 26 17:28:27 2026
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Command: iqtree -s /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa -te tmp.csubst.nwk -m ECMK07+F+R4 --seqtype CODON1 --threads-max 1 -T AUTO --ancestral --rate --redo --prefix /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa
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Seed: 693358 (Using SPRNG - Scalable Parallel Random Number Generator)
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Time: Wed Mar 4 11:11:32 2026
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Kernel: SSE2 - auto-detect threads (12 CPU cores detected)
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Reading alignment file /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa ... Fasta format detected
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Reading fasta file: done in 0.00137806 secs using 91.94% CPU
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Reading fasta file: done in 0.00157714 secs using 74.63% CPU
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Alignment most likely contains DNA/RNA sequences
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Converting to codon sequences with genetic code 1 ...
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Alignment has 33 sequences with 417 columns, 405 distinct patterns
1616
388 parsimony-informative, 14 singleton sites, 15 constant sites
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Gap/Ambiguity Composition p-value
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Analyzing sequences: done in 2.31266e-05 secs using 86.48% CPU
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Analyzing sequences: done in 2.40803e-05 secs using 78.9% CPU
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1 Anolis_carolinensis_ENSACAG00000003255 0.00% failed 0.00%
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2 Astyanax_mexicanus_ENSAMXG00000007127 0.00% passed 86.24%
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3 Bos_taurus_ENSBTAG00000000894 0.00% passed 99.67%
@@ -55,34 +55,32 @@ Reading input tree file tmp.csubst.nwk ... rooted tree
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NOTE: 28 MB RAM (0 GB) is required!
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Measuring multi-threading efficiency up to 1 CPU cores
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4 trees examined
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Threads: 1 / Time: 1.229 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -20897
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Threads: 1 / Time: 1.105 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -17770
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BEST NUMBER OF THREADS: 1
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Estimate model parameters (epsilon = 0.010)
62-
1. Initial log-likelihood: -15505.420
63-
2. Current log-likelihood: -13440.786
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3. Current log-likelihood: -13226.275
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4. Current log-likelihood: -13213.524
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5. Current log-likelihood: -13212.687
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6. Current log-likelihood: -13212.589
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7. Current log-likelihood: -13212.570
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Optimal log-likelihood: -13212.563
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Nonsynonymous/synonymous ratio (omega): 0.088
71-
Transition/transversion ratio (kappa): 1.906
72-
Site proportion and rates: (0.007,0.320) (0.024,0.336) (0.523,0.615) (0.446,1.499)
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Parameters optimization took 7 rounds (32.168 sec)
62+
1. Initial log-likelihood: -13672.031
63+
2. Current log-likelihood: -13349.849
64+
3. Current log-likelihood: -13287.140
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4. Current log-likelihood: -13284.171
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5. Current log-likelihood: -13284.156
67+
Optimal log-likelihood: -13284.152
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Nonsynonymous/synonymous ratio (omega): 1.000
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Transition/transversion ratio (kappa): 1.000
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Site proportion and rates: (0.009,0.265) (0.032,0.379) (0.759,0.828) (0.200,1.785)
71+
Parameters optimization took 5 rounds (15.563 sec)
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Wrote distance file to...
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BEST SCORE FOUND : -13212.563
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BEST SCORE FOUND : -13284.152
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Ancestral state probabilities printed to /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa.state
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Empirical proportions for each category: 0.000 0.000 0.571 0.429
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Empirical proportions for each category: 0.000 0.000 0.835 0.165
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Site rates printed to /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa.rate
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Total tree length: 8.904
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Total tree length: 7.570
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Total number of iterations: 0
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CPU time used for tree search: 0.000 sec (0h:0m:0s)
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Wall-clock time used for tree search: 0.000 sec (0h:0m:0s)
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Total CPU time used: 33.367 sec (0h:0m:33s)
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Total wall-clock time used: 34.065 sec (0h:0m:34s)
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Total CPU time used: 17.113 sec (0h:0m:17s)
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Total wall-clock time used: 17.267 sec (0h:0m:17s)
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Analysis results written to:
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IQ-TREE report: /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa.iqtree
@@ -91,4 +89,4 @@ Analysis results written to:
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Ancestral state: /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa.state
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Screen log file: /Users/kf/Library/CloudStorage/GoogleDrive-kenji.fukushima@nig.ac.jp/My Drive/psnl/repos/csubst/csubst/dataset/PGK.alignment.fa.log
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Date and Time: Thu Feb 26 17:29:01 2026
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Date and Time: Wed Mar 4 11:11:49 2026

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