Result difference between blastall -p blastp (legacy blast) and blastp -task blastp (blast+)

Question

[ahsan.chattha15]

I am new to bioinformatics

I am running pancoreplot in cmg biotools.

I am trying to replace BLASTALL with BLAST+.

Here is the command of BLASTALL:

blastall -F 0 -i a.fsa -p blastp -e 1e-5 -m 7 -d b.fsa | tigrcut | gawk '{print $1"\t"$2}' > blastresult_ab.txt

I have tried to replace this command with BLAST+ command as follows:

blastp -task blastp -query a.fsa -evalue 1e-5 -outfmt 5 -db b.fsa | tigrcut | gawk '{print $1"\t"$2}' >output_ab.txt

But the end results are wrong. I am unable to correctly calculate the core and pan genomes after replacing BLASTALL with BLAST+.

Any help regarding this would be very helpful.

Thanks in advance.