[BUG] IQ2MC crashes with signal segmentation fault

[linaruem]

Dear IQ-TREE developers,

I am attempting to generate a Hessian file for PAML using the IQ2MC strategy, as my analysis involves a partitioned alignment with mixed substitution models. I have run the following command multiple times via a job script submitted to our HPC system:

iqtree -s superaln.fa -p superaln.nex -te superaln.treefile --dating mcmctree --prefix test -nt 64

Unfortunately, each run terminates with a segmentation fault. The job consistently stops near the end of execution, and the attached log file shows error messages at that point. The SLURM job output reports:

/tmp/slurmd/job15153243/slurm_script: line 13: 152129 Segmentation fault (core dumped)

This suggests that the crash occurs around lines 12–13 of the IQ-TREE execution within the job script.

On the other hand, I did not encounter any issues with standard tree inference using IQ-TREE. For example, the following command completed successfully:

iqtree -s superaln_filtered.fa -p superaln.nex -nt 64 -bb 100000

I would greatly appreciate any advice or suggestions on how to diagnose or resolve this issue. Thank you very much for your time and support.

Kind regards,
Lina

test.log

[bqminh]

@piyumalanthony Can you have a look?

[maepz]

I am having a similar issue