Question: makeblastdb won't run in terminal (Mac OS X)
0
gravatar for alexille5640
9 months ago by
alexille564010
alexille564010 wrote:

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.

sequencing blast alignment ncbi • 524 views
ADD COMMENTlink modified 9 months ago by WouterDeCoster36k • written 9 months ago by alexille564010
1

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.

ADD REPLYlink written 9 months ago by WouterDeCoster36k

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

ADD REPLYlink written 9 months ago by alexille564010
4
gravatar for RamRS
9 months ago by
RamRS20k
Houston, TX
RamRS20k wrote:

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.

ADD COMMENTlink modified 9 months ago • written 9 months ago by RamRS20k

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

ADD REPLYlink written 9 months ago by alexille564010
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