Can you show a working script in code blocks? Also it would help to put the output in separate code blocks. See Writeup Formatting Tips.

Working Code

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use Expect;
use Net::OpenSSH;
use Log::Log4perl qw(:easy);



#Initializing the log file..
my $log_file = "/tmp/linux_cmd_execute_".$id.".log";
Log::Log4perl->easy_init(
    {
        level => $INFO,
        file  => "> $log_file",
    }
    );


INFO( "expect usage user - $user 
      host - $host , fuser - $fuser , cmd - $cmd ");


my $start_time = time();


INFO("ssh to the host $host");
my $ssh = Net::OpenSSH->new("$user:$pswd\@$host");
if($ssh->error) {
    print "Unable to connect $host " . $ssh->error;
    exit;
}

my $expect;

    my ( $pty, $pid ) = $ssh->open2pty( { stderr_to_stdout => 1 }, "su
+do su - $fuser" )
      or die "Failed to attempt sudo su - $fuser";
    $expect = Expect->init($pty);

$expect->exp_internal(1);
$expect->log_file("/tmp/expect.log", "w");

my $before;
my $exit1;
my $output;
my $result = $expect->expect(
    undef,
    [
        "\[\r\n]?\[^\r\n]+\[%#>\$] \$",
        sub {
            my $self = shift;
            INFO("Sending command $cmd");
            $self->send("ls \r");
        }
    ]
) or custom_error( "Expect Failed ",$id);



$expect->hard_close();

exit 0;
[download]

-----this output i need in a file------
Starting EXPECT pattern matching...
 at /usr/local/share/perl5/Expect.pm line 597
        Expect::expect('Expect=GLOB(0x2b70d80)', undef, 'ARRAY(0x2b712
+18)') called at /products/backend/mopgenie/expect3.pl line 86
handle id(9): list of patterns:
  #1: -re `[\r\n]?[^\r\n]+[%#>$] $'


handle id(9): Does `'
match:
  pattern #1: -re `[\r\n]?[^\r\n]+[%#>$] $'? No.

handle id(9): Does `\033]0;user@host:~\007\033[?1034h[user@host ~]$ '
match:
  pattern #1: -re `[\r\n]?[^\r\n]+[%#>$] $'? YES!!
    Before match string: `'
    Match string: `\033]0;user@host:~\007\033[?1034h[user@host ~]$ '
    After match string: `'
    Matchlist: ()
Calling hook CODE(0x2b70cd8)...
Sending 'ls1;date \r' to handle id(9)
 at /usr/local/share/perl5/Expect.pm line 1421
        Expect::print('Expect=GLOB(0x2b70d80)', 'ls1;date \x{d}') call
+ed at /products/backend/mopgenie/expect3.pl line 84
        main::__ANON__('Expect=GLOB(0x2b70d80)') called at /usr/local/
+share/perl5/Expect.pm line 825
        Expect::_multi_expect(undef, undef, 'ARRAY(0x1f52480)') called
+ at /usr/local/share/perl5/Expect.pm line 602
        Expect::expect('Expect=GLOB(0x2b70d80)', undef, 'ARRAY(0x2b712
+18)') called at /products/backend/mopgenie/expect3.pl line 86
Starting EXPECT pattern matching...
 at /usr/local/share/perl5/Expect.pm line 597
        Expect::expect('Expect=GLOB(0x2b70d80)', undef, 'ARRAY(0x2b72a
+40)') called at /products/backend/mopgenie/expect3.pl line 122
handle id(9): list of patterns:
  #1: -re `[\r\n]?[^\r\n]+[%#>$] $'
[download]

It looks like you are using two log files. Does either show anything?

I've downloaded and am trying to execute the code. Can you please define ALL missing undefined vars (use bogus names if necessary to disguise sensitive data)?. Thanks.

-Tom

Update: Please also include your "custom_error" subroutine.

Update2: I'm making a bit of progress, but I believe it would help more if you could describe plainly what you are trying to accomplish with your script. Using Expect is a last resort IMHO--to be used ONLY when human interaction is needed. There may be a better way to handle your problem. For one thing you might check out auditd.