No Alignment In The Output Of Blastn

Question

[Anima Mundi]

Hello everybody, I am trying to BLAST a nucleotide query against a nucleotide database via command line.

The problem is that, when I try blastall -p blastn -d mydatabase -i myquery I get just:

BLASTN 2.2.25 [Feb-01-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= myquery
         (52 letters)

Nothing else is displayed, even when trying to make positive control experiments. What is wrong?

Thanks in advance.

[PoGibas]

Have you tried blasting your sequences on ncbi server? Just to check if they are ok.

[Anima Mundi]

I just tried, it works on NCBI.

[PoGibas]

Consider this answer - A: Help with formatdb and blast all (blastall vs blastn)

[Anima Mundi]

Thanks; actually, I was trying to use blastall to avoid a problem in the format of my subject database while using blastn. Maybe I will open a new question to fix that issue.

[Anima Mundi]

Here is the new question: Database error when running blastn