I'm unfamiliar with how to annotate a bedpe file with the GENOCDE gtf file:

https://www.gencodegenes.org/releases/25.html

My understanding is to use bedtools intersect, but I'm getting errors:

http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

Here is the format of my (unsorted) bedpe, file1.bedpe:

 chrom1     start1       end1       chrom2    start2       end2      info
0       1     6469       68470      1         8609         8610      abc3 
1       1     8426       8627       5         1076796      1076797   abc3  
2       1     14632      14933      1         142491       142492    abc3     
3       16   16570       166971     1         167720       167721    abc3    
4       1     104384     104985     1         10461        10472     abc3

There are a few more categorial columns (i.e. strand, and other information)

When I try

bedtoools intersect -a file1.bedpe -b gencode.v25.annotation.gtf

I get the error

ERROR: file `file1.bedpe`: has non positional records, which are only valid for the groupBy tool.

What is the correct way to do this?