Hi,

I require embl files for a pipeline I am using. With all my samples I have done the same thing - downloaded fasta files, annotated using Prokka, used gff3toembl to convert the gff to an embl (I need the gff file for a different pipeline). It has been fine for almost all my samples, however for a small number of my samples the embls created are separated still by contigs. So in one strains embl file, there are multiple smaller embl files for each contig. This means for my pipeline it only sees the first contig.

Does anyone know why this is or how to fix this?

Thanks