Running with "general" db requires vog.annotations.tsv which is absent from hmm/

lukesarre commented 1 year ago

Hi, there. Thank you for developing this wonderful tool.

I was trying to get Viral Recall up and running using the general VOG database, but ran into the error:

Traceback (most recent call last):
  File "viralrecall.py", line 733, in <module>
    status = main()
  File "viralrecall.py", line 728, in main
    run_program(input, project, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, 
summary_file, contiglevel)
  File "viralrecall.py", line 383, in run_program
    vdesc = get_annot(database)
  File "viralrecall.py", line 41, in get_annot
    input = open("hmm/vog.annotations.tsv", "r")
FileNotFoundError: [Errno 2] No such file or directory: 'hmm/vog.annotations.tsv'

As I understand, this should be present in the hmm/ folder from Zenodo as per the README, but it isn't there. Can you direct me where to find it, or help find an alternative?

Thank you for your help,

Regards,

Luke

lukesarre commented 4 months ago

Hiya, just bumping this as I'm coming back to this project and it would be a big help to use the general database! Thank you again for maintaining this tool Luke

faylward commented 4 months ago

I have updated the tarball and download link, so please try this again and see if it works. Best, Frank

On Fri, Jul 5, 2024 at 7:18 AM lukesarre @.***> wrote:

Hiya, just bumping this as I'm coming back to this project and it would be a big help to use the general database! Thank you again for maintaining this tool Luke

— Reply to this email directly, view it on GitHub https://github.com/faylward/viralrecall/issues/23#issuecomment-2210694066, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPFN7UXQFD62EXTWVOCECTZKZ6HDAVCNFSM6AAAAABKNAPTTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQGY4TIMBWGY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Frank O. Aylward Assistant Professor Department of Biological Sciences Virginia Tech Blacksburg, VA

lukesarre commented 4 months ago

That's great - all is working. Thanks Frank!

faylward / viralrecall

Running with "general" db requires vog.annotations.tsv which is absent from hmm/ #23