Note that this way, the spacing needs to be exactly the same for this to work. Also note that had PLUTO been present in y.txt it would still have been either listed as absent, because of the cut utility's single space separator, if the spacing were different, or listed as present on the basis of column 1 only and the exactly two spaces after it.

IMO, a more robust way is to use the spacing tolerance of for example awk plus exact string matching :

Code:

awk 'NR==FNR{A[$1,$2]; next} !(($1,$2) in A)' y.txt x.txt

or the other way around:

Code:

awk 'NR==FNR{A[$1,$2]; next} !(($1,$2) in A)' x.txt y.txt