The system called prokka doesn't have '--compliant' option. Due to this, when there are long contig names, the LOCUS line in the .gbk file is unrecognised by this tool. A fix is to change prokka run command as follows:
command = prokka_path+" %s --compliant --outdir %s --prefix %s --kingdom %s --force"%(fasta_file,outdir,prefix,kingdom)
The system called prokka doesn't have '--compliant' option. Due to this, when there are long contig names, the LOCUS line in the .gbk file is unrecognised by this tool. A fix is to change prokka run command as follows: command = prokka_path+" %s --compliant --outdir %s --prefix %s --kingdom %s --force"%(fasta_file,outdir,prefix,kingdom)
Hope this helps someone for troubleshooting..