"D:\Program Files\foo.exe" arg1 arg2 "file_name with spaces.txt"
[download]

I suppose I should refresh my knowledge before writing anything that makes use of that feature myself.

So something like this:

my $command = “c:\\blast\bin\\blastall.exe" -p blastn -d "$hu_seq $hd_seq" -i "$contig" -o $alignment”;
print "$command\n";
system($command);

Better:

my @command = ("c:\\blast\bin\\blastall.exe",
   -p => 'blastn',
   -d => "$hu_seq $hd_seq",
   -i => $contig,
   -o => $alignment,
);
system(@command);
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Note: You've got a problem if -d expects space-separated paths if the paths have spaces in them.

You are missing putting delimiters around the whole thing.

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