Intersectbed Tool Generating Empty File

I have used the Bedtools command intersectBed to check the overlap between two bed files. A is my INDEL file and B is my Reference file. But it is producing an empty output file. I thought the problem was that the file B is much larger than file A. But I tried changing the file order and it is still not creating any output.

Here is the reference B file (larger):

gff_seqname      0        1395    gene    0    +
gff_seqname      0        1395    exon    0    +
gff_seqname    1397    2498    gene    0    +
gff_seqname    1397    2498    exon    0    +
gff_seqname    2524    3619    gene    0    +

Here is my A file with just 51 INDELS:

NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME    174708    174713    -GCCGG:2/6
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME    1078686    1078686    +A:105/112
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME    1229123    1229125    -CT:800/870
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME    1234830    1234830    +AT:134/134
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME    1234833    1234834    -A:134/134

here is my command:

intersectBed -a SOD_pal_BWA_GMM.PE.sorted.bam.sorted_cleaned_GMM.bam.sorted.hr.bam.raw.bed  -b sodalis_galaxy.bed  -wa -wb  >test13.bed