Blast Database error

Question

[ksi216]

Hi, I'm new to unix and I am having trouble running blast. this is what I'm getting

http://postimg.org/image/srbf5e0v5/

Answer 1

[Philipp Bayer]

You supplied the database est_human.aa which from the rest of the screenshot doesn't seem to be in the folder /home/BI7533/ncbi-blast-2.2.31+/db, you have only a est_human database in there.

I'm not really sure what you're trying to do - est_human.aa implies that you want to blast against amino-acids/proteins, but you're using the command blastn (nucleotide blast), not blastp (protein blast). The est_human database you have there is a nucleotide database (it ends in nsd, nin, nhr, nal, the protein databases like swissprot end in pni, pnd, etc.)

[ksi216]

I just want to run that file against the est_human database. Im not sure of the syntax for the command. I want it to run against every file that has est_human. How would I do this ?

[GenoMax]

Use -db /path_to/est_human (you do not need to specify any suffix) in addition to other options you want to use for blast.

[ksi216]

Command line argument error:

Argument "query". File is not accessible: `41o5.fa

thats what I got now.

[GenoMax]

Post the full command you are using if you want additional help.

That error seems to indicate that the file in question is not readable/available in $PATH.