Already checked the logs: Nothing helpful. As I mentioned previously I discovered the problem using a proprietary application and creating my own script just confirmed there was an issue with large files getting cut off which perhaps suggests there is a problem with the environment. I followed the sample on this page: http://www.perlfect.com/articles/perlfile.shtml for reading in a large file line-by-line. I don't believe it's a problem with the data file itself - I have tried changing the input data used and the problem is reproducible and also, as I mentioned previously the point at which the file gets cut of seems arbitrary (it's not always the same place in the file).