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$ cat 1028930_short
2
5
6
8

$ cat 1028930_long
1
...
7
8
9

$ perl -i -nE 'chomp; if ($s) { $d{$_} or say } else { ++$d{$_}; ++$s 
+if eof; say }' 1028930_short 1028930_long

$ cat 1028930_short
2
5
6
8

$ cat 1028930_long
1
...
4
7
9