but $alignment is a Perl file handle (that you explicitly opened), and you can't pass Perl file handles to other programs via system() arguments...  Maybe you just want to pass the respective output filename instead (the one you used in the open())? 

...
my $alignment = "$maid_dir\\${maid}_aln.out";
my $command = qq(c:\\blast\\bin\\blastall -p blastn -d "$hu_seq $hd_se
+q" -i $contig -o $alignment);

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In reply to Re^3: quoting issue with system command by almut
in thread quoting issue with system command by lomSpace

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