Your post is far too long and verbose for me to read in its extension. But you have at least conveniently marked the problematic line:

system $merker2;
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Never run system without checking its result:

system $merker2 == 0
    or die "Couldn't launch [$merker]: $!/$?";
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... or, if you want to continue even though the external command failed/was not launched, just output a warning instead. Maybe consider putting all those system() calls into one central routine that logs the command, runs it and outputs errors:

sub run_command {
    my ($cmd) = @_;
    warn "Running [$cmd]\n";
    system($cmd) == 0
        or die "Couldn't launch [$cmd]: $!/$?";
};
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