Oh, I am using it on Windows. My path is :

$hu_seq is 'I:\13414 Ccl9 (88)\sequencing\13414_hu.fa'
$hd_seq is 'I:\13414 Ccl9 (88)\sequencing\13414_hd.fa'

This is what I am passing to the system command.
my @command2 =('c:\\blast\\bin\\blastall.exe','-p', 'blastn','-d',"$hu_seq $hd_seq",'-i', $contig,'-o', $alignment);

I am getting the following error message:

NULL_Caption ERROR: Could not open i:\13414
NULL_Caption ERROR: Arguments must start with '-' (the offending argument #7 was: 'Ccl9')

I think that this is why I am unable to build the blastsearchable db.
How do I get around those space in path to the variable?
Thanks!
LomSpace