Welcome, @llau! I believe the issue here is that your HPC system is using an ASCII (not UTF-8) locale (like C) but the assign-colors.py script assumes a UTF-8 locale (like en_CA.UTF-8).
For troubleshooting purposes, can you run the locale command on your HPC system and paste the output here?
The long-term fix is to update the assign-colors.py script to be explicit about its file encoding instead of assuming the locale’s encoding will be UTF-8. As a workaround in the meantime, however, you can try running snakemake after overriding the default locale to use a UTF-8 one. For example:
LC_ALL=en_CA.UTF-8 snakemake --cores 1 --profile ./my_profiles/getting_started
We fixed a similar issue in Augur itself earlier this year, but your problem seems to be within the ncov-specific assign-colors.py.
Let me know what locale says and if the workaround above works for you?