You seem to be running the same command two times, just to have its output stored in two distinct output files. Apart from that, I'd be worried about the risks of running shell commands that way, unless there is very hight certainty that the perl variables being used to build the command are "safe" (contain no shell metacharacters, etc).

In any case, it seems like you only need a shell to run the initial part of your pipeline, and it would be just as well for perl to do the rest:

my @command = ( $swlist, '-l', 'depot', '@', $depot_locn );
my $child_pid = open( my $shell, '-|', @command )
    or die "shell command failed: $!\n";

open( my $out1, ">>", $log_std_depot ) or die "$log_std_depot: $!\n";
open( my $out2, ">>", $temp_log ) or die "$temp_log: $!\n";

print $out1 "COMMAND: @command  ## FILTERS: $rel_string / $i / AR\n";

while (<$shell>) {
    next unless ( /$rel_string/ and /$i/ and /AR/ );
    print $out1 $_;
    print $out2 $_;
}
close $out1;
close $out2;
close $shell;
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Update: note that by doing the "grep" parts inside perl, you are able to make use of perl's much more powerful regex syntax -- you can do things that would not be possible with the standard command-line grep tool.

Another update: changed the code snippet to open the two output file in append mode (>> as per the OP code) rather than "truncate" mode.