I downloaded nr locally and am trying to BLAST my fasta files against the nr database. I don't get an error but when I check the out file it looks as though it stops early. It stops at the first run and doesn't do a comparison, only prints the reference names, version, and the 1st query. I'm using...
blastall -p blastn -d nr -i inputfile.fasta -o output.out
Is it not finding nr to make a comparison to?
I downloaded the "per-formatted" databases from NCBI, and after unpacking have .phd .phi .phr .pin .pnd .pni .pog .ppd .ppi .psd .psi and .psq files. Are these per-formatted?
Oh, I think I have a better picture of what's going on. You're using "blastn" against "nr," which is a nucleotide search against a protein database. If you're trying to do a protein search, use "blastp." If you are trying to do a nucleotide search, try the "nt" database.
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide
It says that nr is under the "Nucleotide Databases for BLAST" section. Which should I download then for nucleotides? I tried telling update_blastdb.pl nt but it said nt was not found.
I was running it in virtual box, that is why it would not find nt.
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I'm not sure if this is related to your issue, but the 'blastall' program has been deprecated. The newer versions are a little easier to work with, as a nice bonus. http://www.biostars.org/post/show/1557/help-with-formatdb-and-blast-all/#1558
I tried using it without blastall in the format from the link you gave me and it said it could not find blastn even when I gave the direct path.
I know for sure it is because of the database. I removed the -d option and got the same result, which means it is not finding the locally downloaded pre-formatted NCBI database. how can I get it to find local nr?