Version:
3.0.1 (Linux x86 64-bit, built May 5 2025)
Problem:
IQ-TREE 3.0.1 crashes during ModelFinder with +ASC on a variable-sites-only alignment. The crash occurs at modelfactory.cpp:1131 every time ModelFinder hits its first duplicate model entry. Reproducible across multiple runs, different model sets, and two different input files with the same properties. The assertion itr != checkpoint->end() fails in ModelFactory::initFromNestedModel.
Commands:
iqtree3 -bb 5000 -st DNA -m MFP+ASC -nt 8 -s ADMIXTURE.250.final.min4.phy.varsites.phy -redo
# restricted to GTR models
iqtree3 -m TESTONLY+ASC -st DNA -nt 8 -s ADMIXTURE.250.final.min4.phy.varsites.phy -redo
Both crash at the first duplicate model:
MFP+ASC: crashes at model 14 (duplicate of model 3, JC+ASC+R2)TESTONLY+ASC: crashes at model 4 (duplicate of model 2, JC+ASC+G4)
Error:
ERROR: modelfactory.cpp:1131: virtual bool ModelFactory::initFromNestedModel(std::map<...>):
Assertion `itr != checkpoint->end()' failed.
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
Possibly related — sequence type misidentification:
Both runs produce this warning despite -st DNA being explicitly set:
Alignment most likely contains protein sequences
WARNING: Your specified sequence type is different from the detected one`
Not sure if the latter is related to the crash, but I'm including it since it appears consistently.
Alignment:
- Variable sites only (.varsites.phy), generated by IQ-TREE from a larger SNP alignment (LD-pruned with PLINK prior to tree building)
- 27 sequences, 232,915 columns, 200,723 distinct patterns
- 159,372 parsimony-informative sites, 73,543 singleton sites, 0 constant sites
- 25/27 sequences fail composition chi2 test (p < 5%)
- No checkpoint file present at time of crash (-redo used)
I included the log files for both runs below.
iqtree3_MFP+ASC_crash.txt
iqtree3_TESTONLY+ASC_crash.txt
Version:
3.0.1 (Linux x86 64-bit, built May 5 2025)
Problem:
IQ-TREE 3.0.1 crashes during ModelFinder with +ASC on a variable-sites-only alignment. The crash occurs at modelfactory.cpp:1131 every time ModelFinder hits its first duplicate model entry. Reproducible across multiple runs, different model sets, and two different input files with the same properties. The assertion itr != checkpoint->end() fails in ModelFactory::initFromNestedModel.
Commands:
Both crash at the first duplicate model:
MFP+ASC: crashes at model 14 (duplicate of model 3,JC+ASC+R2)TESTONLY+ASC: crashes at model 4 (duplicate of model 2,JC+ASC+G4)Error:
Possibly related — sequence type misidentification:
Both runs produce this warning despite
-st DNAbeing explicitly set:Not sure if the latter is related to the crash, but I'm including it since it appears consistently.
Alignment:
I included the log files for both runs below.
iqtree3_MFP+ASC_crash.txt
iqtree3_TESTONLY+ASC_crash.txt