mpoelchau

Thanks for the bug report, @chklopp ! We'll look into this in the next couple of days. In the meantime, would you be willing to share the datasets/command you used...

Hi @thierryjanssens, just checking in - did the above suggestion solve your problem?

Hi @yanzhongsino. How is the mRNA modeled? If there are exon features in addition to CDS, I'd recommend using `gff3_to_fasta -st user_defined -u mRNA exon`. But that really depends on...

@yanzhongsino when you say that you only got the CDS fasta at first - do you mean that you only got the sequences for the individual CDS segments (e.g. in...

Thanks for the response @yanzhongsino (and sorry about the delay). I'm curious - are the nucleotide sequences that you got from the different commands this same (mRNA vs. CDS)?

@DiegoSafian apologies, I completely missed this issue. Can you try removing the locus features from your gff3 file, to see if that is what the ID generator is erroring out...

@MesYosra Sorry about the issues. Are you able to share a snippet (or all) of the gff3 so I can debug? Thanks!

Thanks for sharing the file @MesYosra. I am not sure why this is not working for you. The -uuid option works (instead of the -diglen + -idpre options) - will...

I ran the program as follows with the file that you provided, and obtained the attached output. I am not sure why it didn't add IDs in your case. Were...

@MesYosra sorry, we don't have enough people right now to support this. Perhaps you could ask the Braker developers to support providing IDs for all feature types.