illegal instruction & ValueError("Expected 'query_file' or 'query_ids', or 'query_profiles'")

[FranziNMicrobio]

Hello,

I would really like to use cblaster because it sounds so useful for what I'm trying to do. Unfortunately, I seem to struggle with it at nearly every step.

Firstly, when I stalled it via pip, I always get an error saying "illegal instruction", despite the installation being successful:

...

Successfully installed cblaster-1.3.19 (base) E-LOSX9MVQP:cblaster p91134fn$ cblaster config --email franziska.nagel@postgrad.manchester.ac.uk Illegal instruction: 4 (base) E-LOSX9MVQP:cblaster p91134fn$ cblaster -h Illegal instruction: 4 (base) E-LOSX9MVQP:cblaster p91134fn$ cblaster --help Illegal instruction: 4

I had more luck when I installed is using mamba as described here: https://bioconda.github.io/recipes/cblaster/README.html

So, for example, I successfully manages to create a database for a local search using makedb, although not entirely without error messages:

But when I then want to do a search, another set of errors comes up:

I've tried many variations of the code at this point but the program just doesn't seem to be working for me.

Can someone help? I would really like to use this program for a publication I am currently working on.

Many, many thanks in advance.

Best wishes,
Franziska

[gamcil]

Sorry for taking so long to see this. Did you manage to resolve the issue? I'm not sure about the illegal instruction error, that seems like it could be related to something installed in your local environment, hence why installing via mamba likely worked here. You can ignore the error message about genomicsqlite, this is an optional library (can be installed with conda install -c mlin genomicsqlite) which is used to make the generated SQLite database smaller - if it isn't installed, cblaster just uses the default built in library instead.
The search issue is weird since there is nothing wrong with your command. It is possible that cblaster just failed to parse your FASTA file correctly and thus threw that error, in which case I would have to look at the file and see what is happening there.