Problems when running mmseqs

Question

[Yarabi]

Hello. I am doing viral RNA sequence mapping using mmseqs. When I do this I get the following message:

Input database "concat_prove.fasta" has the wrong type (Generic)
Allowed input:
- Index
- Nucleotide
-Profile
- Aminoacid

This is the code I used:

mmseqs search "concat_prueba.fasta" database result-out tmp-folder

I already generated my indexed database and the concatenation of my FASTA files.

Could you please help me?

[Ram]

Please stop using bioinformatics or bioinformatic as tags. Every single post on this forum is related to bioinformatics, so that tag adds zero value. I've removed it from your previous post as well as this one, please be more careful in the future.

[GenoMax]

Both target and query databases need to be converted by createdb per the manual. You have done this already? Based on the error above you probably have not done this for the concatenated fasta.

[Yarabi]

I just did it but it keeps giving me an error.

Input database "database" has the wrong type (Generic)
Allowed input:
- Index
- Nucleotide
-Profile
- Aminoacid

[GenoMax]

Not a mmseq user but you should not include concat_prueba.fasta in command? This is the example from manual.

mmseqs search queryDB targetDB outDB tmp

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time - actually, I've done it for you at least twice by this point.

[Philipp Bayer]

What does concat_prove.fasta look like? There's a known bug around some RNA datasets https://github.com/soedinglab/MMseqs2/issues/611