facing issue with custom database about vapid HOT 3 CLOSED

I was facing the same problem, it's hardcoded that there's a "|" separation in reference names and that the 4th field when you do line.split("|")[3] returns the accession number.
You have two choices, change your database sequence names to fit that criterion, or change line 106 so it returns the accession number

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Hi! Sorry for missing the first post and thanks for the solution posted above!

You can also use the —f flag to specify a specific reference file that you would like to use. So in this case you could download NC_045512.2.gbf once and then use the —f flag to always annotate off that file. This completely skips the blast search and is a good option once you know the reference you’re using works well for your files.

How exactly did you create your reference database? Could you upload it? I’d like to take a look and ensure that people can easily make their own reference databases and use them without modifying the code. I’m glad this tool seems like it would be useful and I want to make sure it works for everyone!
R

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Hey, thanks for the response.

I think the problem is easy to fix, it's just that in the database you have, the references' names have a | separation and the 3rd field (0 index) is the accession number, however, if someone builds their own database (Like I did where I replaced all the NCBI viral reference already in all_viruses with a newer version and added covid, I downloaded the viral.1.1.genomic from NCBI, and the names didn't have | separation anymore and the code breaks), so the problem is just in the naming.

However, I did encounter some minor problems in the code and fixed them. I will try to fix a couple of things and send you a pull request, then if you think the fixes make sense, feel free to merge then :)

I'll try to do it in the near future :)

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