Entering edit mode
8.0 years ago
linhuixinnn
•
0
Hi,
I am new to this whole command line Blast+ Suite. Sorry for sounding dumb but I couldnt find useful help sheet online. I am trying to build a localized database from a taxa group nucleotide and protein. I followed the instruction and typed:
makeblastdb -in chl.fasta.txt -input_type fasta -parse_seqids -dbtype nucl -out /db/bast/chldb
There was error makeblastdb command not found. How do I rectify this?
I am using Mac OS Terminal.
Thank you.
To be more explicit take a look at this page from the link @Istvan posted below: https://www.biostarhandbook.com/book/computer/how-to-set-the-path.html
I tried but it still cannot work. Please kindly guide.
You need to specify what it is that you tried (post commands, error messages etc) in order for us to be able to guide you.
I will provide one hint. You installed the blast package in a directory that is not in your $PATH. You have two options while running makeblastdb. You can either amend your $PATH (as indicated in the help link) or provide full path for the makeblastdb executable when you try to run it.
i entered to the dir with the makeblastdb exe file. i typed makeblastdb -help. the error message is makeblastdb command not found too. is it because i didnt install properly?
Spend a bit of time to get some basics of UNIX under your belt by following this course here.
Even if you are in the directory where the makeblastdb executable is you won't be able to run it by just using the name. You will need to explicitly indicate that it is in the current directory by doing
$ ./makeblastdb -hi typed ./makeblastdb -h. the error is Illegal instruction
That tells me that you likely downloaded blast binaries for a different OS (perhaps linux). You should download the binaries for OS X (which would be the .mg file: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+.dmg ).
Also take a look at this NCBI blast tutorial that was just posted on Biostars.
Oh indeed. I will add this answer to the handbook as well.
It is a common error especially that there may be 32 bit and 64 binaries, plus Mac and Linux.
Unfortunately, this link doesn't work anymore.
This is a standard operation. Here is one link that should help: https://stackoverflow.com/questions/14637979/how-to-permanently-set-path-on-linux-unix
the book has changed a lot in the meantime, the content is all there but under different pages