I've tried to make a subset of pre-formated blast database with blastdb_aliastool from ncbi-blast-2.3.0+. It failed on nt but success on nr. I pretty sure the file is intact, because I've check the md5sum. Here's a quick sample:

#retrieve data
wget http://ftp.ncbi.nlm.nih.gov/blast/db/nt.00.tar.gz
wget http://ftp.ncbi.nlm.nih.gov/blast/db/nr.00.tar.gz
tar -xf nt.00.tar.gz
tar -xf nr.00.tar.gz

#get some gi to test
blastdbcmd -db nr.00 -entry all|head|grep "^>"|sed -e 's/>gi|//g' -e 's/|.*//g' > nr_gi.txt
#success
blastdb_aliastool -gilist nr_gi.txt -db nr.00 -out nr_gi
#check alias db content
blastdbcmd -db nr_gi -entry all

#get some gi to test
blastdbcmd -db nt.00 -entry all|head|grep "^>"|sed -e 's/>gi|//g' -e 's/|.*//g' > nt_gi.txt
#failed
blastdb_aliastool -gilist nt_gi.txt -db nt.00 -out nt_gi
#check alias db content
blastdbcmd -db nt_gi -entry all

It failed with this message:

Converted 2 GIs from nt_gi.txt to binary format in nt_gi.p.gil
BLAST Database error: BLASTDB alias file creation failed.  Some referenced files may be missing

Why blastdb_aliastool only works on nr? Some post said specify -parse_seqids when makeblastdb should work(it is also nr). Then I tried:

# try makeblastdb first
blastdbcmd -db nr.00 -entry all|head -n 1000 > nr_test.fa
makeblastdb -in nr_test.fa -dbtype prot -parse_seqids -out nr_test
#success
blastdb_aliastool -gilist nr_gi.txt -db nr_test -out nr_gi_test
#check alias db content
blastdbcmd -db nr_gi_test -entry all

blastdbcmd -db nt.00 -entry all|head -n 1000 > nt_test.fa
makeblastdb -in nt_test.fa -dbtype nucl -parse_seqids -out nt_test
#failed again
blastdb_aliastool -gilist nt_gi.txt -db nt_test -out nt_gi_test
#check alias db content
blastdbcmd -db nt_gi_test -entry all

It's still not working. I found another post, which seems nt is also working. Was It related to the blast+ version? How to make alias db with blastdb_aliastool on nt correctly?