Running workflow using RefSeq genomes instead of Ensembl

[MauriAndresMU1313]

Great for your workflow, really useful guide to perform Genome Annotation.
Unfortunately, I got stuck in the step 4c. Create CDS-only annotation bed file, because I only obtain empty files. I think that I know the reason, so here is my hypothesis.

I'm using genomes from RefSeq, and so far in a lot of examples, if not all, I found that the genome annotation relies on genomes from Ensembl, which of course have another notation related to the IDs.

So, I started running the script WriteChromLengthBedFromFasta.py, using a *_genomic.fna file from the following link. For example, that file only contains a fasta file with the sequence of chromosome 1. After the conversion, my new bed file looks like this:

NC_000001.11	0	248956422
NT_187361.1	0	175055
NT_187362.1	0	32032
NT_187363.1	0	127682
NT_187364.1	0	66860
NT_187365.1	0	40176
NT_187366.1	0	42210
NT_187367.1	0	176043
NT_187368.1	0	40745
NT_187369.1	0	41717

The second column contains only 0. This output made me understand that at some point I got an empty file because the information was incorrect, why I say that?, because other examples available contain 0 and other numbers, so my question is:

• What do you think is happening?
• Did anyone try to run this with RefSeq genomes too?
• Do I need to use another .fna file?

I really want to avoid changing to Ensembl genomes, because I had a lot of work already done with RefSeq data.
Any comment about what could be the source of the issue is more than welcome!