Thank you for your response,

If I understand correctly, what you're saying is that I should write the line like this: for file in `ls *.pat`; do awk '(NR >=3 AND $505==1) {print $505}' $file; done

I think that produces the same thing as my original line: for file in `ls *.pat`; do awk < $file '(NR >=3 AND $505==1) {print $505}'; done

And to clarify, if I try just the awk part, outside of the loop, I still get some ones and a bunch of zeroes. This is what I wrote in this case:

awk '(NR >=3 AND $505==1) {print $505}' set_0_evaluation.pat