Codeml has been killed when running the software.

Skip to first unread message


Mar 18, 2024, 4:22:28 AMMar 18
to PAML discussion group
When I set up the .pml and .tree file, run the software, it gives an error, is there anyone in the same situation, can you tell me how to solve it.
Here are my two files, along with the error code.
Thank you very much.

Sandra AC

Mar 18, 2024, 10:44:08 AMMar 18
to PAML discussion group
Hi there,

It looks like there are various formatting issues in your input files:

1) The format of your alignment file is not a PHYLIP format. You should have the tag ID of your sequences (i.e., the "tag" or "identifier" you use to name your sequence) separated by at least two spaces from their corresponding sequence (i.e., protein sequences in your case). In addition, the tag IDs you use to identify 68 taxa are not the same tags you used in your tree file (they need to be the same or PAML programs will abort). In addition, your tag IDs have spaces and are longer than they should be.
2) Your tree file lacks the PHYLIP header (i.e., <num_taxa  1>, first type the number of taxa, introduce one or two spaces, then type `1` as you only have one tree).

You can check the PAML Wiki on the GitHub repository and check the dedicated section on Data Formatting to make sure that your alignment and tree files are in the correct format next time that you try to run PAML programs :)

In addition, I would suggest that you run PAML programs from the terminal instead of using the outdated PAML-X Gui.

Hope this helps!
Reply all
Reply to author
0 new messages