Your original sed line is missing a quote. If you want to call the same line through system, you have to quote it, but there is no need to quote the slashes or commas. Another problem is the variable $file: if it is a Perl variable, you should not put it into signle quotes, as they do not interpolate variables, but doulbe quotes do. If it is a shell variable, make sure it exists in the subshell started by system.

system "sed -n -e '/log-passed/,/log-end/p' /var/log/app1/$file"; # Pe
+rl variable
[download]

Update: It is still a mystery why you cannot let Perl do all the work:

open my $FH, '<', "/var/log/app1/$file" or die $!;
while (<$FH>) {
    print if /log-passed/ .. /log-end/;
}
[download]

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