I can not see any error on your original script, maybe the problem is on the called script "mycode.pl". You should try to make your script work without any paralelism first: 
my @list = glob("*.fasta");
foreach my $fname (@list) {
  my ($base) = split /\./, $fname;
  system "perl mycode.pl $base >~/MyPerl/result_ans/$base.out"
}

[download]
and later, once you have it working, add the Proc::Queue bits: 
use Proc::Queue size=>5, qw(system_back);

my @list = glob("*.fasta");
foreach my $fname (@list) {
  my ($base) = split /\./, $fname;
  system_back "perl mycode.pl $base >~/MyPerl/result_ans/$base.out"
}
1 while wait != -1;

[download]
You can also activate Proc::Queue trace mode to see what's going on.

In reply to Re: Running a Perl Code within a Perl Code Using "Shell Module" by salva
in thread Running a Perl Code within a Perl Code Using "Shell Module" by monkfan

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