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Cannot download DB of viruses #689

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ruqaiyatasneem opened this issue Apr 4, 2024 · 1 comment
Open

Cannot download DB of viruses #689

ruqaiyatasneem opened this issue Apr 4, 2024 · 1 comment

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@ruqaiyatasneem
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ruqaiyatasneem commented Apr 4, 2024

I am new to bioinformatics field and I wanted to try prokka so I installed it and it says I have to run prokka --setupdb during that it says
Error: File existence/permissions problem in trying to open CM file /home/ruqaiya/.local/lib/prokka/db/cm/Viruses. CM file /home/ruqaiya/.local/lib/prokka/db/cm/Viruses not found (nor an .i1m binary of it)
I am installing it on conda on WSL

Screenshot (748)
`which cmpress
/usr/bin/cmpress
cmpress -h

cmpress :: prepare an CM database for faster cmscan searches

INFERNAL 1.1.4 (Dec 2020)

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Usage: cmpress [-options]

Options:
-h : show brief help on version and usage
-F : force: overwrite any previous pressed files
ls -lsa /usr/local/bin/../db/cm/Viruses
ls: cannot access '/usr/local/bin/../db/cm/Viruses': No such file or directory`

@7feeling
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7feeling commented Jul 9, 2024

@ruqaiyatasneem Use this '$HOME/prokka/bin/prokka --setupdb' command as it written at the main page and try to use all needed commands in such format '$HOME/prokka/bin/prokka --options <filename.fasta>'

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