I know nothing about BLAST files, but it's probably because

my $blastcut = substr $blastline, 7;

is sometimes an empty string. Maybe do something like this:

if ($blastline =~ /$ender/ && $headerline =~ /\Q$blastcut\E/) {

or this:

my $printing = 0;
while (<BLASTFILE>) {
   if (/Query=\s*(.*)/) {
      $printing = (index($headerline,$1) >= 0);
   }
   print if $printing;
}

[download]

In reply to Re: Extracting BLAST hits from a list of sequences by no_slogan
in thread Extracting BLAST hits from a list of sequences by Oligo

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