Problems with blastn execution from command line

[angeloulivieri]

Hi all,
I have the n-th problem with blast. This time it's blastn that is destroying my days..

I use the blast+ (ncbi-blast-2.2.27+).

I simply have downloaded an RFAM db and used makeblastd on it:

with this command:

../ncbi-blast-2.2.27+/bin/makeblastdb -in rRNA.fa -dbtype 'nucl'

and this output:
Building a new DB, current time: 10/03/2012 11:30:22
New DB name: rRNA.fa
New DB title: rRNA.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Ignoring sequence 'lcl|149850' as it has no sequence data
Adding sequences from FASTA; added 153329 sequences in 12.7754 seconds.


So I created a nucleotide database for use with my fasta file. Queries are ATGC type.

Then I run the blastn command on a file with 100 sequences:

../ncbi-blast-2.2.27+/bin/blastn -query longTestSeq.fasta -db data/rRNA.fa -out outBlastn100s



And this is part of the outputfile:

BLASTN 2.2.27+


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.
Database: rRNA.fa
153,329 sequences; 77,423,059 total letters

Query= comp173253_c0_seq1
Length=1717
***** No hits found *****
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 123848567440

Query= comp174620_c0_seq1
Length=1566
***** No hits found *****

Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 113092217700

............and a lot of other NO HITS FOUND.

Why this happens?

I'm almost sure to have used the correct nucleotide database and queries. If you want I can cut and paste some of the sequences for each of them.

Please help me!
Thanks

[angeloulivieri]

Ok! There is nothing wrong! Now I know that since blastn is used to know about contaminations in the transcriptome... having NO HIT is meaning that my sequences doesn't.

bye