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