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PatrickRWright / CopraRNA

Target prediction for prokaryotic trans-acting small RNAs
MIT License
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Genome not available even if present in CopraRNA_available_organisms.txt #33

Closed gprezza closed 3 years ago

gprezza commented 3 years ago

Hi there,

I'm trying to run CopraRNA locally, but I keep running into the problem that one genome I have in my input file is not available.

https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP040530 is present in the prokaryotes.txt NCBI file and even in CopraRNA's _CopraRNA_availableorganisms.txt file: grep "NZ_CP040530" ~/bin/CopraRNA/update_kegg2refseq/run/CopraRNA_available_organisms.txt gives: NZ_CP040530 NZ_CP040529 Bacteroides_thetaiotaomicron

However, when I run CopraRNA, I get the error: Error: 'NZ_CP040530' is not present in the availability list and is thus not compatible with CopraRNA.

Am I missing something?

PatrickRWright commented 3 years ago

Hi there,

its been a long time since I last looked into CopraRNA but I assume you need to copy those files into the coprarna_aux directory in your local copy. The directory you are looking at in your grep statement is the example to run the update for the availability files. Once you have updated the files, you need to copy them over to coprarna_aux. I hope that makes sense and helps.

The README actually also explains this: https://github.com/PatrickRWright/CopraRNA#update-coprarna-available-organisms

Cheers, Patrick

gprezza commented 3 years ago

Oh you're right! I missed that part of the README. Thanks!

PatrickRWright commented 3 years ago

No worries. I'm glad it helped.