![enter image description here][1]


  [1]: https://img.techpowerup.org/190813/screenshot-23.png

Hi,
I am doing reciprocal blast to find ortholog. for that i run i create database and run blastn and retrieve hit sequence fasta through  awk 'BEGIN { OFS = "\n" } { print ">"$2, $3 }' blast.out > hit.fa
but when i am trying to align hit.fa to reference genome database, i am getting this issue. 

I used this command.--

blastn -query ~/Blast/hit.fa -db ~/Blast/omykiss/genome/omykiss -outfmt 6 -out blast_out -num_alignments 1


please help to solve it. 

Thanks in advance



Hyphens (coding for indels relative to another sequence, from BLAST in this case) are not in {A, C, G, T, N}. You should remove them or replace them with Ns, depending on what you're trying to do.

A [quick Google search][1] reveals this was an issue in some other applications, as well.


  [1]: https://github.com/wwood/singlem/issues/17