You have the right idea, in collecting data into your (hopefully declared earlier) arrays : @data1, @data2 etc.

The problem area is when you open and write to the output file WITHIN the read loop for each row.

You need to move the output file open and Write OUTSIDE the file read loop, something like this:

# Outside the read loop, after closing input file....
mkdir "$pathname" or die "Error couldn't create new Directory";
open my $OUT1, ">", "$pathname/column.txt" or die "error couldn't open
+ output file";

print $OUT1 "$_\n" for @data1;

close $OUT1;
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(Made some adjustments to localize the file handle, and use the "3 argument" open - see other writeups to understand why this is a good idea.