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my @list = glob("*.fasta");
foreach my $fname (@list) {
  my ($base) = split /\./, $fname;
  system "perl mycode.pl $base >~/MyPerl/result_ans/$base.out"
}

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use Proc::Queue size=>5, qw(system_back);

...
  system_back "perl mycode.pl $base >~/MyPerl/result_ans/$base.out"
}
1 while wait != -1;