I don't think so, but if I'm wrong, I would be happy because I miss it too. What I'm doing now is (works with a tab delimited output and a multifasta file query) to find the last query ID written in the blast output, and then to find it into the fasta file. This works only because sequences are "blasted" in the same order as in the query file.
## 1st step
tail -1 out.tab.blast | cut -f 1 > lastqueryblasted
## 2nd step
grep -n -f lastqueryblasted query.fasta
# res1, ex: 23000
## last step, pourcentage computing
wc -l query.fasta
# res2, ex: 33000
# your (under)estimated pourcentage
echo "(23000 / 33000) *100" | bc -l
This is not very convenient I know, but it helps.
EDIT: I use that so much often, that I eventually wrapped it in a script.
If you name it
blast_monitor.sh, it works like this:
blastab_monitor.sh blastresult.blast queryfasta.fa
Here it is:
### monitor a tab-outputed blast job by giving the approximative % done
echo "the blast out is: "$blast
echo "the fasta query is: "$query
curquery=$(tail -1 $blast | cut -f 1)
curline=$(fgrep -n $curquery $query | cut -f 1 -d ':')
nblines=$(wc -l $query | cut -f 1 -d " ")
percent=$(echo "($curline/$nblines) *100" | bc -l | cut -c 1-4)
echo "The blast job is about $percent % done..."
I hope that helps.