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

Question

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 many unnecesary 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 80?????
   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 I get the following error.

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

I have 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.

Does anybody knows the probable reason of this error?

Thank you very much for your help.

Answer 1

You're trying to use a Blast+ option with the legacy program blastall. Try installing blast+ and running the blastn program

Answer 2

I don't think there is a parameter for minimum percent identity. There are options to limit the output results to X number of hits.

Percent identity isn't even that useful because it doesn't take into account the length of the hit. e-value which takes the identity AND the length into account to give you the probability that the alignment occurred by chance.

Usually, I think what people usually do is get the hits back and take the best X hits based on e-value. Remember, the lower the e-value the better.