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Couldn't build blast database #176

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itaysol opened this issue Jan 12, 2025 · 1 comment
Open

Couldn't build blast database #176

itaysol opened this issue Jan 12, 2025 · 1 comment

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@itaysol
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itaysol commented Jan 12, 2025

Hi, I'm trying to run mob typer using thos snakemake rule:

rule run_mobtyper:
    
conda:
        "envs/mob_suite.yaml"
   
 input:
        os.path.join(output_dir,"results","plasmids_concat.txt")
   
 output:
        os.path.join(output_dir,"results","mob_typer.txt")
   
 log:
        "logs/mobtyper.log"
   
 params:
        mobDB = mobsuiteDB
    
shell:
        """
        mob_typer --multi --infile {input} --out_file {output}
        """

and although I download the database using this sh file:

mkdir databases/mob_suite
wget https://zenodo.org/records/10304948/files/data.tar.gz?download=1
tar --xzf data.tar.gz > databases/mob_suite/
rm data.tar.gz?download=1
    

I get this error:

ERROR: Could not build blast database, check error messages..cannot continue

I tried running mob_init with specyfing the db directory with no success.
Any thoughts about that?
Thanks in advance, Itay.

@kbessonov1984
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You might be missing BLAST dependency. You can also install MOB-Suite database via mob_init and them point to that database directory via the -d option. Also you can copy entire database from Docker or Singularity image

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