gat-compare, not identifying shared annotations between count files

[qianxidu]

Hello,

I am having issues running gat-compare.py on my regions. The output log of gat-compare says that there are no shared annotations between my count files, even though I definitely used the same annotation bed file to generate both count files. I have attached the count files below. I have also attached the output log file.

This is the code I used:
gat-compare.py anchorGAT_1_nucleotide-overlap.counts.tsv.gz anchorGAT_2_nucleotide-overlap.counts.tsv.gz

This is how I generated the count files:
gat-run.py --num-threads=4 --num-samples=1000 -s /home/qiadu/GATdata/RT_TADs/anchors_GAT/anchorset_forGAT_1.bed -a /home/qiadu/GATdata/RT_TADs/anchors_GAT/con.early.bed -w /home/qiadu/GATdata/RT_TADs/merged.genome.bed --log=GAT_1.log --output-counts-pattern=anchorGAT_1_%s.counts.tsv.gz

gat-run.py --num-threads=4 --num-samples=1000 -s /home/qiadu/GATdata/RT_TADs/anchors_GAT/anchorset_forGAT_2.bed -a /home/qiadu/GATdata/RT_TADs/anchors_GAT/con.early.bed -w /home/qiadu/GATdata/RT_TADs/merged.genome.bed --log=GAT_2.log --output-counts-pattern=anchorGAT_2_%s.counts.tsv.gz

anchorGAT_1_nucleotide-overlap.counts.tsv.gz
anchorGAT_2_nucleotide-overlap.counts.tsv.gz
gat-compare_anchor_output.txt

Any help would be appreciated. I might just be missing something obvious. Thank you.
Cheers,
Qian