Having a challange to compare models for snp phylogenetic inference

[henok-bot]

The errror log file

IQ-TREE version 3.0.1 for Linux x86 64-bit built Jul 9 2025
Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren
Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow,
Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt

Host: data (AVX512, FMA3, 62 GB RAM)
Command: iqtree3 -s trypanosoma_iqtree.varsites.phy -st DNA -mset GTR,HKY -m TEST+ASC -bb 1000 -alrt 1000 -T 8 --prefix>
Seed: 12345 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Jan 7 06:34:50 2026
Kernel: AVX+FMA - 8 threads (8 CPU cores detected)

Reading alignment file trypanosoma_iqtree.varsites.phy ... Phylip format detected
Alignment most likely contains protein sequences
WARNING: Your specified sequence type is different from the detected one
Constructing alignment: done in 0.523965 secs using 64.44% CPU
Alignment has 25 sequences with 246389 columns, 151194 distinct patterns
138863 parsimony-informative, 107526 singleton sites, 0 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 0.0122186 secs using 782.3% CPU
1 SRR6052131_sorted 48.99% failed 0.17%
2 SRR6052132_sorted 47.14% failed 2.42%
3 SRR6052133_sorted 41.89% passed 57.07%
4 SRR6052134_sorted 38.56% failed 0.00%
5 SRR6052135_sorted 48.26% failed 2.94%
6 SRR6052136_sorted 43.72% passed 62.53%
7 SRR6052137_sorted 28.60% failed 0.29%
8 SRR6052138_sorted 48.50% failed 0.41%
9 SRR6052139_sorted 48.72% failed 1.05%
10 SRR6052140_sorted 51.40% failed 0.56%
11 SRR6052141_sorted 29.38% passed 91.09%
12 SRR6052142_sorted 24.84% failed 0.02%
13 SRR6052143_sorted 24.85% failed 0.02%
14 SRR6052144_sorted 29.99% passed 92.52%
15 SRR6052145_sorted 45.73% passed 53.83%
16 SRR6052146_sorted 44.95% passed 41.07%
17 SRR6052147_sorted 40.04% passed 19.75%
18 SRR6052148_sorted 45.29% passed 57.51%
19 SRR6052149_sorted 31.24% failed 2.39%
20 SRR6052150_sorted 39.27% passed 96.27%
21 SRR6052151_sorted 34.25% passed 50.71%
22 SRR6052152_sorted 44.98% passed 27.93%
23 SRR6052153_sorted 44.31% passed 35.98%
24 SRR6052154_sorted 41.22% passed 35.89%
25 SRR6052155_sorted 43.78% passed 86.59%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
**** TOTAL 40.40% 11 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: minimal branch length is reduced to 0.000000405862 for long alignment
Checking for duplicate sequences: done in 0.0619831 secs using 119.1% CPU

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.347 seconds
Perform fast likelihood tree search using GTR+ASC model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.532929 secs using 796.5% CPU
Estimate model parameters (epsilon = 1.000)

1. Initial log-likelihood: -1554021.202
2. Current log-likelihood: -1554018.018
   Optimal log-likelihood: -1554017.852
   Rate parameters: A-C: 0.98837 A-G: 3.11279 A-T: 0.81279 C-G: 0.54525 C-T: 3.10054 G-T: 1.00000
   Base frequencies: A: 0.237 C: 0.261 G: 0.257 T: 0.245
   Parameters optimization took 2 rounds (0.776 sec)
   Time for fast ML tree search: 4.549 seconds

NOTE: ModelFinder requires 1067 MB RAM!
ModelFinder will test up to 8 DNA models (sample size: 246389 epsilon: 0.100) ...
No. Model -LnL df AIC AICc BIC
1 HKY+ASC 1556457.544 48 3113011.087 3113011.106 3113510.991
2 HKY+ASC+G4 1555583.351 49 3111264.701 3111264.721 3111775.020
4 HKY+F+ASC+G4 1555768.996 52 3111641.991 3111642.014 3112183.554
ERROR: modelfactory.cpp:1131: virtual bool ModelFactory::initFromNestedModel(std::map<std::__cxx11::basic_string,>
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 1 funcAbort()
ERROR: 2 ()
ERROR: 3 pthread_kill()
ERROR: 4 gsignal()
ERROR: 5 abort()
ERROR: 6 ()
ERROR: 7 ModelFactory::initFromNestedModel(std::map<std::__cxx11::basic_string<char, std::char_traits, std::all>
ERROR: 8 CandidateModel::evaluate[abi:cxx11](Params&, ModelCheckpoint&, ModelCheckpoint&, ModelsBlock*, int&, int)
ERROR: 9 CandidateModelSet::test(Params&, PhyloTree*, ModelCheckpoint&, ModelsBlock*, int, int, std::__cxx11::basic_s>
ERROR: 10 runModelFinder(Params&, IQTree&, ModelCheckpoint&, std::__cxx11::basic_string<char, std::char_traits,>
ERROR: 11 startTreeReconstruction(Params&, IQTree*&, ModelCheckpoint&)
ERROR: 12 runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&)
ERROR: 13 runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 14 main()
ERROR: 15 ()
ERROR: 16 __libc_start_main()
ERROR: 17 ()
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: trypanosoma_iqtree.log
ERROR: *** Alignment files (if possible)

vcf2phyl_output_to_phylotree_iqtree.sh: line 70: 84292 Aborted (core dumped) iqtree3 -s "trypanosoma_iqtree.varsites.phy" -st DNA -mset GTR,HKY -m TEST+ASC -bb 1000 -alrt 1000 -T "$THREADS" --prefix "$PREFIX" -seed "$SEED" --redo

[thomaskf]

Hi, Thanks for posting the issue. This looks like a known issue that has been fixed in the current development version. Could you please download the latest source code from GitHub (https://github.com/iqtree/iqtree3), recompile IQ-TREE, and try running the analysis again? If the problem persists with the latest code, please let us know and include the new log file so we can investigate further. From: Henok Tadesse Bireda ***@***.***> Date: Wednesday, 7 January 2026 at 5:42 pm To: iqtree/iqtree2 ***@***.***> Cc: Subscribed ***@***.***> Subject: [iqtree] Having a challange to compare models for snp phylogenetic inference (Discussion #510) The errror log file IQ-TREE version 3.0.1 for Linux x86 64-bit built Jul 9 2025 Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt Host: data (AVX512, FMA3, 62 GB RAM) Command: iqtree3 -s trypanosoma_iqtree.varsites.phy -st DNA -mset GTR,HKY -m TEST+ASC -bb 1000 -alrt 1000 -T 8 --prefix> Seed: 12345 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Jan 7 06:34:50 2026 Kernel: AVX+FMA - 8 threads (8 CPU cores detected) Reading alignment file trypanosoma_iqtree.varsites.phy ... Phylip format detected Alignment most likely contains protein sequences WARNING: Your specified sequence type is different from the detected one Constructing alignment: done in 0.523965 secs using 64.44% CPU Alignment has 25 sequences with 246389 columns, 151194 distinct patterns 138863 parsimony-informative, 107526 singleton sites, 0 constant sites Gap/Ambiguity Composition p-value Analyzing sequences: done in 0.0122186 secs using 782.3% CPU 1 SRR6052131_sorted 48.99% failed 0.17% 2 SRR6052132_sorted 47.14% failed 2.42% 3 SRR6052133_sorted 41.89% passed 57.07% 4 SRR6052134_sorted 38.56% failed 0.00% 5 SRR6052135_sorted 48.26% failed 2.94% 6 SRR6052136_sorted 43.72% passed 62.53% 7 SRR6052137_sorted 28.60% failed 0.29% 8 SRR6052138_sorted 48.50% failed 0.41% 9 SRR6052139_sorted 48.72% failed 1.05% 10 SRR6052140_sorted 51.40% failed 0.56% 11 SRR6052141_sorted 29.38% passed 91.09% 12 SRR6052142_sorted 24.84% failed 0.02% 13 SRR6052143_sorted 24.85% failed 0.02% 14 SRR6052144_sorted 29.99% passed 92.52% 15 SRR6052145_sorted 45.73% passed 53.83% 16 SRR6052146_sorted 44.95% passed 41.07% 17 SRR6052147_sorted 40.04% passed 19.75% 18 SRR6052148_sorted 45.29% passed 57.51% 19 SRR6052149_sorted 31.24% failed 2.39% 20 SRR6052150_sorted 39.27% passed 96.27% 21 SRR6052151_sorted 34.25% passed 50.71% 22 SRR6052152_sorted 44.98% passed 27.93% 23 SRR6052153_sorted 44.31% passed 35.98% 24 SRR6052154_sorted 41.22% passed 35.89% 25 SRR6052155_sorted 43.78% passed 86.59% WARNING: 1 sequences contain more than 50% gaps/ambiguity **** TOTAL 40.40% 11 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: minimal branch length is reduced to 0.000000405862 for long alignment Checking for duplicate sequences: done in 0.0619831 secs using 119.1% CPU Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.347 seconds Perform fast likelihood tree search using GTR+ASC model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Optimizing NNI: done in 0.532929 secs using 796.5% CPU Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -1554021.202 2. Current log-likelihood: -1554018.018 Optimal log-likelihood: -1554017.852 Rate parameters: A-C: 0.98837 A-G: 3.11279 A-T: 0.81279 C-G: 0.54525 C-T: 3.10054 G-T: 1.00000 Base frequencies: A: 0.237 C: 0.261 G: 0.257 T: 0.245 Parameters optimization took 2 rounds (0.776 sec) Time for fast ML tree search: 4.549 seconds NOTE: ModelFinder requires 1067 MB RAM! ModelFinder will test up to 8 DNA models (sample size: 246389 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 HKY+ASC 1556457.544 48 3113011.087 3113011.106 3113510.991 2 HKY+ASC+G4 1555583.351 49 3111264.701 3111264.721 3111775.020 4 HKY+F+ASC+G4 1555768.996 52 3111641.991 3111642.014 3112183.554 ERROR: modelfactory.cpp:1131: virtual bool ModelFactory::initFromNestedModel(std::map<std::__cxx11::basic_string,> ERROR: STACK TRACE FOR DEBUGGING: ERROR: 1 funcAbort() ERROR: 2 () ERROR: 3 pthread_kill() ERROR: 4 gsignal() ERROR: 5 abort() ERROR: 6 () ERROR: 7 ModelFactory::initFromNestedModel(std::map<std::__cxx11::basic_string<char, std::char_traits, std::all> ERROR: 8 CandidateModel::evaluate[abi:cxx11](Params&, ModelCheckpoint&, ModelCheckpoint&, ModelsBlock*, int&, int) ERROR: 9 CandidateModelSet::test(Params&, PhyloTree*, ModelCheckpoint&, ModelsBlock*, int, int, std::__cxx11::basic_s> ERROR: 10 runModelFinder(Params&, IQTree&, ModelCheckpoint&, std::__cxx11::basic_string<char, std::char_traits,> ERROR: 11 startTreeReconstruction(Params&, IQTree*&, ModelCheckpoint&) ERROR: 12 runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&) ERROR: 13 runPhyloAnalysis(Params&, Checkpoint*) ERROR: 14 main() ERROR: 15 () ERROR: 16 __libc_start_main() ERROR: 17 () ERROR: ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: *** For bug report please send to developers: ERROR: *** Log file: trypanosoma_iqtree.log ERROR: *** Alignment files (if possible) vcf2phyl_output_to_phylotree_iqtree.sh: line 70: 84292 Aborted (core dumped) iqtree3 -s "trypanosoma_iqtree.varsites.phy" -st DNA -mset GTR,HKY -m TEST+ASC -bb 1000 -alrt 1000 -T "$THREADS" --prefix "$PREFIX" -seed "$SEED" --redo — Reply to this email directly, view it on GitHub<#510>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AENQCRSZYPPDZJPVZEGHOW34FSTGDAVCNFSM6AAAAACQ5FF5BKVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZZGMYTMNZSGY>. 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