Unrelated to your problem, but for reliability and security, I would recommend the 3+ argument form of open,

open(MYFILE, "-|", "/bin/zcat", $myfile) || die("ERROR: Cannot open $m
+yfile for read: $!\n");
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Or better use a lexical scalar,

my $fh;
if ($myfile =~ /\.gz$/)
{
    open($fh, "-|", "/bin/zcat", $myfile) || die("ERROR: Cannot open $
+myfile for read: $!\n");
}
...
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