IQ-TREE CRASHES WITH SIGNAL ABORTED

[sttongjai]

Hello,

I was trying to use IQ-Tree 3 to construct a tree from SNPs of core genomes. The command line was as follow.

$ ./iqtree-3.0.1-Linux/bin/iqtree3 -s ./KD_Elizabethkingia_20250908_PC/PhyloPanaroo20251009/ClinicalCMEA_CoreGenesAlignment_SNP.fasta -m MFP --wbtl -B 1000

However, an error occurred during a ModelFinder step, and an error message was _"ERROR: modelfactory.cpp:1131: virtual bool ModelFactory::initFromNestedModel(std::map<std::__cxx11::basic_string, std::vector<std::_cxx11::basic_string > >): Assertion `itr != checkpoint->end()' failed."

I have attached a log file. Please let me know how to solve this problem.

Thank you very much.

Siripong

ClinicalCMEA_CoreGenesAlignment_SNP.fasta.log

[ljz3216]

I am also running into this issue, please help me resolve it, thank you.

[TSZUoE]

Hey,

I was having a similar issue when running an alignment file from Gubbins:
iqtree -s file.aln -B 1000

But providing a model "-m GTR" fixed the issue for me