The intersection tool under "Operate on Genomic Intervals (bx)" is not working for returning either overlapping regions or overlapping pieces. The intersection and overlaps in the non-bx operations section are working. I was running intersection (bx) on a set of Mathieu Blanchette's PReMods (118,402 regions) with our RP>0.05 intervals (314,040 regions), in hg17, requiring at least 10bp overlap. Here are the error messages. For returning overlapping pieces: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_intersect.py", line 63, in ? main() File "./tools/new_operations/gops_intersect.py", line 56, in main for line in intersect([g1,g2], pieces=pieces, mincols=mincols): File " For returning overlapping regions: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_intersect.py", line 63, in ? main() File "./tools/new_operations/gops_intersect.py", line 56, in main for line in intersect([g1,g2], pieces=pieces, mincols=mincols): File " I'll leave the files and results in my history for a while in case that is helpful. Thanks, Ross Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8@psu.edu phone: 814-863-0113 FAX: 814-863-7024