Where do you use the 'Double RegEx'? Currently, your entire code could be rewritten as:
chomp @lines;
foreach (@lines) {
    next unless /^>/;
    push @chromoLine, $_ if (split /\|/)[4] =~ /\Q$Homosapiens\E/;
}

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Paul

In reply to Re: Double RegEx by rev_1318
in thread Double RegEx by MonkPaul

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