error message after tree construction and asr analysis with codon models ("ERROR: File not found MG")

[Gabriel DUPRE]

Hi,

I had trouble when launching a tree construction and an asr analysis with providing codon models (MG+F1X4+R7 and MG+F3X4+R6).
With both of the two types of jobs, I received the same error message (see below). I am wondering if that IQtree interprets the "-m" option as an input file name, and that seems quite weird to me.

Job1:
Command_job1 (tree_construction): iqtree -s alignement_file -m MG+F1X4+R7 -alrt 1000 -b 100 -redo -nt 8
ERROR: File not found MG


Job2:
Command_job2 (ASR): iqtree -s alignement_file -m MG+F1X4+R7 -te tree_file -asr
ERROR: File not found MG


Does someone encounter the same problem? How can I perform my jobs with these codon models (MG+F1X4+R7 and MG+F3X4+R6)?

Best regards,

Gabriel

[Minh Bui]

Hi Gabriel,

Simple answer: you forgot to set the sequence type as codon: -st CODON (for standard genetic code; for changing the genetic code see the docs).

Due to this, IQ-TREE assumes you are using a DNA model. Because MG is not in the list of pre-defined DNA models, it assumes that MG is a file name containing a custom model. That’s why it’s trying to read that file, that obviously does not exist.

Cheers

Minh

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