Download of genomes fails when release number and/or assembly type are provided

[vizkidd]

For Ensembl : release version 107, Assembly types : toplevel, primary_assembly Steps to reproduce : Just give a db="ensembl", release=107 and assembly_type="primary_assembly" when invoking getGenome()

Error Produced: Found organism but given release number did not specify existing file

It works fine when these options are not included and the download works properly

[vizkidd]

Forgot to mention,

R version : Both 4.1.1 and 4.2.1

[vizkidd]

Update: There are several organisms which fail and several which work, sus_scrofa doesn't seem to work even though the genome is listed and available through the function is.genome.available()

[HajkD]

Dear Vishvesh,

Many thanks for notifying me.

I can have a look and see if a patch can be provided.

Cheers, Hajk

[Roleren]

Hello, simple answer is that there is no primary assembly for the whole pig genome.

Usually when I use biomartr for this, I make a tryCatch and start with primary, if it fails then I try top-level.

This question can be closed

[HajkD]

Excellent!!! Thank you so much for your insight!