Dear Galaxy, Last night (1AM) and today (10:45AM) I have not been able to return results with the operate on genomic intervals, intersect tool. For example if I upload ChIP-seq peak replicates in .gz format (downloaded directly from ENCODE), no results are returned when they are intersected with each other (or with themselves). If I use the Join tool I indeed am able to join many intervals as would be expected. Not sure if I am doing something wrong this time..... Here is a shared history link to give an example: https://main.g2.bx.psu.edu/u/mdwilson/h/intersect-test Best regards, Mike