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Description
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.
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