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makeblastdb won't run in terminal (Mac OS X)

So I downloaded the BLAST+ executables from NCBI (from here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/).

I opened terminal, copied and pasted the path to where I unzipped the BLAST+ file, and when I try to use makeblastdb I get "command not found"

Here is a screenshot (just blotted out my username): enter image description here

I don't understand why it's not working, the path is correct, all files are there, I downloaded the 64bit version to match my mac.

The reason I'm doing this is because I want to make a local database out of a FASTA file to run a BLAST against. If anyone has any easier way of doing this please share, as my code proficiency is not strong.

blast ncbi sequencing alignment
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updated by WouterDeCoster WouterDeCoster • written by alexille5640 • alexille5640

I edited your title. There is no need to feel bad about asking naive questions when you are a beginner :-)

Try to follow command line tutorials, it will pay of in the long run.

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written by WouterDeCoster WouterDeCoster

Oh haha, well thank you, this is a very friendly community!

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written by alexille5640 • alexille5640

1 answer

Short version: You should use ./makeblastdb not just makeblastdb

Long version: Executables in the current directory are not added to $PATH unless . is in $PATH and the shell is configured to look in pwd as well. You either need to add the full path of the parent dir containing the executable to $PATH or use the absolute/relative path of the executable to run it.

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written by Ram Ram

This worked like a charm! Thank you so much for your expertise, this just helped me generate some invaluable data for my project!!

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written by alexille5640 • alexille5640

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