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
•
written
by
Richard
1 answer
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...
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Blast Alignment Bug
written by Maria K •
What did you set your -word_size to? try 5 if you haven't
Why are you using blastn-short? Your example sequence is 296nt long, this is not particularly short to me.
Forgot to mention some of my sequences are as short as 45bp.
Please post a reproducible example, otherwise we cannot do anything about that.