What might explain the "[blastall] ERROR: Arguments must start with '-'" error in my code?

Question

[joreamayarom]

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.

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

          #-perc_identity 90?????
          blastall -p blastn -d ReferenceGenome -i QuerySequences -G 1 -E 2 -W 15 -F "m D" -U -e 1e-20 -m 8 -a 8 -o NAME.blast.out

But when I try with -perc_identity 90 flag the following error appears:

         [blastall] ERROR: Arguments must start with '-' (the offending argument #4 was: '90')

I proved the flag in several position (after the blastn, after Querygenome, after "m D") and the only thing that changes is the number after the # in the error message.

Does anybody knows the probable reason of this error and how to solve it?

Thank you very much for your help.

Answer 1

[h.mon]

You are mixing BLAST versions. "-perc_identity" works for the newer BLAST+, but you are using legacy BLAST. I don't think legacy BLAST has an option for percent identity, so if you want it, you should download and install BLAST+.

edit: be aware you'll have to change your whole command-line.