[galaxy-user] subtract

Hello, I am using the subtract (whole dataset) tool. I converted my fastq file to tabular with 2 columns: 1. Identifier and 2. sequence. I then "selected (a few) lines that match an expression" from this initial tabular file and am trying to get a final dataset that is devoid of reads with the few selected lines - thus I subtract the dataset of selected lines from the initial dataset. This tool works with I am performing the workflow on a relatively small file (1/50 the size of a whole sequencing experiment) but repeatly fails when I input the full fastq file. Any idea why this is so? Jose