You probably intended to interpolate those variables (single quotes don't): 

my $command = qq(c:\\blast\\bin\\blastall -p blastn -d "$hu_seq $hd_se
+q" -i $contig -o $alignment);

[download]

OTOH, interpolating the file handle $alignment doesn't make much sense... (so what is that -o $alignment supposed to achieve?)

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

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