with the line number as the hash table index

huh, why not just use an array?

my @a;
while (<>) {
   chomp;
   my @rec = split;
   push @a, [ @rec[???, ???, ???] ];
}
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i should store all the desired columns

You keep saying you only want certain columns, yet you don't say which. Again, just use the index of the columns you want for the question marks.