Side notes:

open my $IFILE, '<', $IDFILE || die "Could not open $IDFILE: $!";
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This does not do what you think it does. General rule is: use high precedence logical operators to act on values, low precedence ones for flow control. Otherwise, do not omit parens.

while ( my $ifile_line = <$IFILE> ) {
    my $hits = substr($ifile_line, 0, 6);
    push @id_hits, $hits;
}
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FWIW, this is one of those cases in which slurping is ok:

my @id_hits=map substr($_, 0, 6), <$IFILE>;
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