I iqtree use HKY when I ask for GTR

[EHC2019]

Hi,
I am new here. Thank you for this community.

I am trying to reconstruct a tree from a directory of MSAs using GTR+G (~6000 files, Input data: 1051 sequences with 7758274 nucleotide sites).

However, I get an output tree with the Model: HKY+F (not GTR)
Could you please help me understand what is wrong with my command.
iqtree2 -s pathToAlnDir/ -m GTR+G -B 1000 -T AUTO -ntmax 8 --prefix conGTR

Thank you!

[roblanf]

That command looks OK to me. Can you please post the log file from your run (called something like conGTR.log)? This has a lot more information in it for us to diagnose what the issue is.

[EHC2019]

Thanks. I attach the log . The "passed" lines were removed since the file was too big.

[roblanf]

Huh. I see what you mean. Can you also attach the .iqtree file. In the meantime, please try this analysis with the latest version of IQ-TREE.

I tried your command on a test dataset with the latest version (v2.3.6) and I got a GTR model as expected.

[bqminh]

Confirming this is a bug in iqtree when using -s with a folder of alignments and -m option, then the default model (e.g. HKY for DNA) is applied, instead of the model specified via -m. Thanks for reporting! We will try to fix it in the next release.
As a quick work around, you need to concatenate all alignments in the folder into a single alignment and then run IQ-TREE on the concatenated alignment. The following two command lines will do:

iqtree2 -s pathToAlnDir -ao concat.phy
iqtree2 -s concat.phy .... # insert all other options you want on include in the original command here

[EHC2019]

Thank you for the prompt reply and for the work around!