"Inappropriate ioctl for device" is not the cause of the error since you don't do any ioctl yourself on any device. $! sometimes gets set so a non-zero value even if program works normally (for example, on my machine perl -E'require DBI; say $!' prints No such file or directory).

What you need to do is to inspect the $aln.phi/Phi.out file (it's where PHI's STDOUT ans STDERR were redirected). You can edit line 63 to print $? and $aln.phi if you need to know their values.