Blastn Standalone Simple Query Hanging

Question

[Richard]

I'm using blastn to blast two relatively short sequences (shown below).

I've been asked to do this with BLAST, so I can't consider using another aligner. If I use default parameters, I get my alignment. If I use

-task blastn-short

it freezes and won't return. I am using 2.2.26+. I have done this with about 1000 other sequences without any problem. I guess I could just take out the -short and move on, but I can't understand why blast freezes up. Any ideas?

I am blasting about 100 sequences that look like this...

CAGGTGCAGCTGGTGCAGAGCGGCAGCGAGCTGAAGAAACCTGGCGCCTCCGTGAAGGTG TCCTGCAAGGCCAGCGGCTACACCTTCACCAGCTACGCCATGAACTGGGTCCGCCAGGCC CCAGGCCAGGGACTGGAATGGATGGGCTGGATCAACACCAACACCGGCAACCCCACCTAC GCCCAGGGCTTCACCGGCAGATTCGTGTTCAGCTTCGACACCAGCGTGTCCACCGCCTAC CTGCAGATCTGTAGCCTGAAGGCCGAGGACACCGCCGTGTATTACTGTGCGAGAGA

against a sequence like this...

NNGGAGGTNNNTNTAAGCAGAGCTNTCTGGCTANNTATNNGAACCCCACTGNTTACNGGG CTTATNGAANTTAATACGACTCACTATAGGGGAGACACAAGCTGGCGGCCGCGGTCTCAA AGGCCCACTGCTTACTGCTCGACGATCTGATCAAGAGACAGGATAAGGAGCCGCCACCAT GGAGTTTGGGCTGAGCTGGCTCTTTCTTGTGGCTATTTTAAAAGGTGTCCAGTGTCAGGT GCAGCTGGTGCAGAGCGGCAGCGAGCTGAAGAAACCTGGCGCCTCCGTGAAGGTGTCCTG CAAGGCCAGCGGCTACACCTTCACCAGCTACGCCATGAACTGGGTCCGCCAGGCCCCAGG CCAGGGACTGGAATGGATGGGCTGGATCAACACCAACACCGGCAACCCCACCTACACCCA GGGCTTCACCGGCAGATTCGTGTTCAGCTTCGACACCAGCGTGTCCACCGCCTACCTGCA GATCTGTAGCCTGAAGGCCGAGGACACCGCCGTGTATTACTGTGCGGACTGGTTCGACCC CTGGGGCCAGGGAACCCTGGTCACCGTGTCCTCAGCCTCCACCAAGGGCCCATCGGTCTT CCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCTGCCTGGT CAAGGACTANTNCNNGNNNNNNN

[Philipp Bayer]

What did you set your -word_size to? try 5 if you haven't

[Leonor Palmeira]

Why are you using blastn-short? Your example sequence is 296nt long, this is not particularly short to me.

[Richard]

Forgot to mention some of my sequences are as short as 45bp.

[Michael]

Please post a reproducible example, otherwise we cannot do anything about that.

Answer 1

[Michael]

Works for me, there might be a formatting error in your input (is it valid fasta format?) or some other problem. So if you need more help please post a real reproducible example.

I tried your sequences converted into two fasta files:

$  /usr/local/ncbi/blast/bin/blastn -task blastn-short -query ~/Desktop/query.fas -subject ~/Desktop/reference.fas 
BLASTN 2.2.26+


Query= query

Length=296

Subject= reference

Length=683


 Score =  569 bits (287),  Expect = 7e-167
 Identities = 290/291 (99%), Gaps = 0/291 (0%)
 Strand=Plus/Plus


Query  1    CAGGTGCAGCTGGTGCAGAGCGGCAGCGAGCTGAAGAAACCTGGCGCCTCCGTGAAGGTG  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  236  CAGGTGCAGCTGGTGCAGAGCGGCAGCGAGCTGAAGAAACCTGGCGCCTCCGTGAAGGTG  295

Query  61   TCCTGCAAGGCCAGCGGCTACACCTTCACCAGCTACGCCATGAACTGGGTCCGCCAGGCC  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  296  TCCTGCAAGGCCAGCGGCTACACCTTCACCAGCTACGCCATGAACTGGGTCCGCCAGGCC  355

Query  121  CCAGGCCAGGGACTGGAATGGATGGGCTGGATCAACACCAACACCGGCAACCCCACCTAC  180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  356  CCAGGCCAGGGACTGGAATGGATGGGCTGGATCAACACCAACACCGGCAACCCCACCTAC  415

Query  181  GCCCAGGGCTTCACCGGCAGATTCGTGTTCAGCTTCGACACCAGCGTGTCCACCGCCTAC  240
             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  416  ACCCAGGGCTTCACCGGCAGATTCGTGTTCAGCTTCGACACCAGCGTGTCCACCGCCTAC  475

Query  241  CTGCAGATCTGTAGCCTGAAGGCCGAGGACACCGCCGTGTATTACTGTGCG  291
            |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  476  CTGCAGATCTGTAGCCTGAAGGCCGAGGACACCGCCGTGTATTACTGTGCG  526

More short hits omited...