Beginner problem: how to code protein-coding genes

[lcfcrespo]

Hello all,

I have been trying to start using IQTree for multi-gene analysis, but have been failing at properly coding the protein-coding gene (COI) into the partition input file.
By going through the tutorial of IQTree, I understand the alignment needs to be divisible by 3, and that would lead to retrieving the positions 1, 4, 7, etc, but isn't that only 1 of the possible reading frames? During my previous usage of other software for phylogenetic analysis, I usually specified all 3 possible reading frames as different partitions. As it is, it seems I am being locked into using only one of the reading frames of the protein-coding gene, which, as it turns out, seems to not be the one used for translation, given the number of translational errors detected by IQTree.

I wonder that the solution to my problem might be rather simple, but I can't find it my myself.
Would be most appreciated for any help.

Finally, my input and outputs on this problem:

Using the following partition file:

#nexus
begin sets;
charset part1 = CODON5, 1-657\3;
charset part2 = CODON5, 2-657\3;
charset part3 = CODON5, 3-657\3;
charset part4 = DNA, 659-1399;
end;

I input this run:

Command: C:\Program Files\iqtree-2.4.0-Windows\bin\iqtree2.exe -s C:\Users\Luís Crespo\Documents\Papers\My papers in prep\Cabo Verde\Cheiracanthium\analyses files\Cheiracanthium extra runs\04 - concatenated IQTree\Cheiracanthium.nex -B 1000 -nt AUTO -p C:\Users\Luís Crespo\Documents\Papers\My papers in prep\Cabo Verde\Cheiracanthium\analyses files\Cheiracanthium extra runs\04 - concatenated IQTree\parts.txt

Added the full output as attachment to avoid spamming the many errors obtained.
parts.txt.log

[bqminh]

Marked as duplicate, for some reason this thread is closed --- I don't see it as open