<p>I am trying to pipe a QuerySequences using bash to perform a blastn on a ReferenceGenome. The problem is that I have to many sequences and, to avoid producing a file with to unnecessary registers (memory issues), I want to limit my output to those results with a percent of identity of 90% or higher.</p>

<p>I have run the following script without the flag I am going to mention afterwards and it works perfectly.</p>

<pre>
          #-perc_identity 90?????
          blastall -p blastn -d ReferenceGenome -i QuerySequences -G 1 -E 2 -W 15 -F &quot;m D&quot; -U -e 1e-20 -m 8 -a 8 -o NAME.blast.out</pre>

<p>But when I try with -perc_identity 90 flag the following error appears:</p>

<pre>
         [blastall] ERROR: Arguments must start with &#39;-&#39; (the offending argument #4 was: &#39;90&#39;)</pre>

<p>I proved the flag in several position (after the blastn, after Querygenome, after &quot;m D&quot;) and the only thing that changes is the number after the # in the error message.</p>

<p>Does anybody knows the probable reason of this error and how to solve it?</p>

<p>Thank you very much for your help.</p>

<p>You are mixing BLAST versions. &quot;-perc_identity&quot; works for the newer <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download">BLAST+</a>, but you are using legacy BLAST. I don&#39;t think legacy BLAST has an option for percent identity, so if you want it, you should download and install BLAST+.</p>

<p><strong>edit</strong>: be aware you&#39;ll have to change your whole command-line.</p>
