Error when estimating linked exchangeabilities (GTRpmix)

[mjamy]

Dear IQ-TREE team,

I'm using IQ-TREE v2.3.5 to estimate linked exchangeabilities under the C60 profile mixture model following this tutorial. My alignment has 143 taxa and 7,855 sites.

However, the run crashed almost immediately with the following error:

ERROR: modelprotein.cpp:998: virtual void ModelProtein::init(const char*, std::string, StateFreqType, std::string): Assertion `nxs_model' failed.

I've attached the log file and input files.

Thanks!
Mahwash

iqtree-error.zip

[thomaskf]

Hi Mahwash,

Thanks for your interest in using the new feature.

It should be "CPREV" instead of "cpREV". That means your command should be:

iqtree2 -s concat_143t_32g_prequal_ginsi_bmge.fasta -m GTR20+C60+G4 --link-exchange -te concat_143t_32g_prequal_ginsi_bmge_cpREV-C60-G.treefile -me 0.99 --init-exchange CPREV -nt 20

Thomas

[thomaskf]

Thanks for reporting the issue. We will update the codes so that in the next version, the model name with the small letter will be accepted for the option "--init-exchange". For this version, please use the capital letter for the model name as the option "-init-exchange" input.

[roblanf]

@thomaskf to clarify further, for the current version should all init models be in all caps?

E..g if one wanted to use Q.plant as an initial model in the current version, should it be adjusted to Q.PLANT?

[thomaskf]

@roblanf Yes, for the current version, the init model for the option "--init-exchange" needs to be in all caps (e.g. Q.PLANT instead of Q.plant).