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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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unsuccessful installation? Diamond command not found #506

Open ArchaeologyRoz opened 3 years ago

ArchaeologyRoz commented 3 years ago

Hi,

I'm trying to look at my metagenomic data from an ancient millet sample. This is my first bioinformatics project and I've had no training

Screenshot 2021-08-31 at 12 51 24

so I apologise if my question is a bit basic.

I need a .daa file from diamond for MegaN. I have successfully downloaded MEGAN and it works with some example data. I can't manage to get my millet samples into a daa file though.

I've downloaded diamond but when I try to execute any commands in my terminal I get diamond not found. Perhaps I haven't installed/downloaded properly but I'm not sure what else to do. I've attached a screenshot.

Thanks for your help,

Roz

bbuchfink commented 3 years ago

You need to include the path to the diamond file e.g. ./diamond blastx ....

ArchaeologyRoz commented 3 years ago

Oh thank you!

I am getting an error for "cannot execute binary file"

I also get this when I try to open the diamond download

Roz

bbuchfink commented 3 years ago

You seem to be using a Mac but have downloaded the linux version. On Mac you have to install either using bioconda, homebrew or compile from source (see the Wiki).

ArchaeologyRoz commented 3 years ago

Ah yes, thanks again! I'm in an Ubuntu server now. I'm trying to build the reference database but having an issue with a state on file nr.faa?

Screenshot 2021-08-31 at 15 36 15
bbuchfink commented 3 years ago

It means the file does not exist. Make sure you have the correct path and file name.