First of all thanks for the new version.
I noticed that you introduced $MAXCONTIGIDLEN to check for long contig names.
Is it intended that this is also checked if --compliant option is not set?
So if I have a contig with ID e.g. : "gi|479173639|ref|NC_021021.1|" downloaded from NCBI this is longer than 20 and I have to rename it by setting --locustag and --centre to something short.