$job = "echo '/usr/bin/php5 /path/to/file.php " . $IdYouWantToGive . " false > /dev/null 2>&1' | at now + 1 minute 2>&1";
$exec = system($job);
Build queue by cycling through items
$j = 0;
/* ... { */
$job = "echo '/usr/bin/php5 /path/to/file.php " . $IdYouWantToGiveForJob . " false > /dev/null 2>&1' | at now + " . round(($j+1)/3) . " minute 2>&1";
$j++;
/* } */
atrm $(atq | cut -f1)
Then check completion with atq
.