I encountered a weird problem when I used blast(i'm using blastall 2.2.26).
I have a fasta file with 8 sequences and I'm running blast on it to get the xml output, the problem is I get 1-8 iterations as expected but in addition I get one more empty iteration with iter-num 1 after iteration 8(meaning I have two 1 iteration, one is good the other only have iter-num and statistics).
I have tried to examine the behavior but I can't get absolute results, sometimes it happens and sometimes it don't(it usually happens occasionally on small sets of sequences like 8).
I looked every where searching for an explanation with no success.
I run the command:
blastall -p blastn -g F -q -9999 -i test.fasta -d /bio/db/blast/miRNA_hair -e 0.01 -m 7 -v 1 -b 1 -o ~pmrotem/checks/split_and_merge_blast/check.xml
Here is input(test.fasta) content:
>1 <unknown description>
AAAAAAAGGATGGAGGAAGATCTACCAAGCAAA>2 <unknown description>
AAAAAAGACACCCCCCCCACCACC>3 <unknown description>
AAAAAAGGAAGGAACTGGGACACGGGA>4 <unknown description>
AAAAACTTGGATCCTGGCCGGGCGC>5 <unknown description>
AAAAAGATGAGTGGTGAAAATCTGATC>6 <unknown description>
AAAAAGCTAACACTCACCTGAGTTTTAAAAAACTC>7 <unknown description>
AAAAAGCTCGTAGTTGGATCTTGGGA>8 <unknown description>
AAAAAGCTCGTAGTTGGATCTTGGGATCGAGCGGGCGGTC
And here is the output(check.xml) content:
< ?xml version="1.0" encoding="UTF-8"?>< !DOCTYPE BlastOutpu ...