Off topic:Bedtools and BEDOPS closest/closest-features issues

Question

[ashjay]

I have a bed file with hg19 motif coordinates that I would like to annotate. I downloaded the hg19 refFlat bed file from UCSC and (after sorting both files with the sort function) tried to use the closest function in bedtools to annotate the closest gene. However, I my output only shows the following:

MBP:manual_annotations$ bedtools closest -a sorted.abcd.bed -b sorted.refFlat.bed -d
chr19 940789549407959 E-box-116519    --box-11+805    chr1   
934341  935552  HES4    0   934438  935353  0   4   471,88,96,307,  0,564,730,904,  769
chr19   940789549407959 E-box-116519    --box-11+805    chr1   
934343  935552  HES4    0   934438  935353  0   3   469,88,481, 0,562,728,  769

closest-features in BEDOPS gives me a similar output.

Adding the > to a file just outputs my motif file in its entirety.

Any ideas on what's going on?