blastn Command Not Found

Question

[2Black_Cats]

Hi. I'm working in Terminal on a shared server to look at some WGS data. I need to use abricate and blastn. The professor who "owns" the computer wants things downloaded by her and then used by everyone else, so she created an abricate_users group, which I belong to.

When I try to run abricate --db resfinder, I get ERROR: Could not find 'blastn'. Please install it and ensure it is in the PATH. I've echoed the $PATH for blastn and this is the output: /home/linuxbrew/.linuxbrew/Cellar/blast/2.14.0/bin/blastn:/home/<myusername>/anaconda3/bin:/home/<myusername>/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

I'm able to run the following using the full file path: /home/linuxbrew/.linuxbrew/Cellar/blast/2.14.0/bin/blastn -version, so I know the command can at least be used. Any help in running abricate is greatly appreciated!

Answer 1

[GenoMax]

this is the output: /home/linuxbrew/.linuxbrew/Cellar/blast/2.14.0/bin/blastn:/home/<myusername>/anaconda3/bin:/home/<myusername>/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

$PATH variable needs to point to the directory containing the executable so

/home/linuxbrew/.linuxbrew/Cellar/blast/2.14.0/bin/blastn

should actually be

/home/linuxbrew/.linuxbrew/Cellar/blast/2.14.0/bin/

[2Black_Cats]

Thank you! That solved it, and I was able to run the command.

[Ram]

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