Empty Output Files from find_intersecting_snps.py in WASP ASE Analysis

[chen-t43]

Hello,
I am using WASP to analyze allele-specific expression (ASE). My command is as follows:
python3 find_intersecting_snps.py --is_paired_end --is_sorted --snp_dir ../SNP --output_dir output sample.bam
Here is the relevant portion of the log file:
prefix: output/135dpf_bb_6f.add.bam.rechr
reading reads from: 6.add.bam.rechr.bam
writing output files to:
output/6.add.bam.rechr.remap.fq1.gz
output/6.add.bam.rechr.remap.fq2.gz
output/6.add.bam.rechr.remap.single.fq.gz
output/6.add.bam.rechr.keep.bam
output/6.add.bam.rechr.to.remap.bam

starting chromosome 1
reading SNPs from file '../SNP/1.snps.txt.gz'
processing reads
starting chromosome NW_026521044.1
WARNING: unable to read from file '../SNP/2.snps.txt.gz', assuming no SNPs for this chromosome
processing reads

DISCARD reads:
unmapped: 951802
mate unmapped: 875013
improper pair: 1184709
different chromosome: 424794
indel: 24
secondary alignment: 6277745
supplementary alignment: 0
excess overlapping snps: 0
excess allelic combinations: 0
read pairs with discordant shared SNPs: 0
missing pairs (e.g. mismatched read names): 0

KEEP reads:
single-end: 0
pairs: 15916157

REMAP reads:
single-end: 0
pairs: 0

read SNP ref matches: 0
read SNP alt matches: 0
read SNP mismatches: 0
And I got results :
6.add.bam.rechr.to.remap.bam
6.add.bam.rechr.keep.bam
6.add.bam.rechr.remap.fq1.gz
6.add.bam.rechr.remap.fq2.gz
6.add.bam.rechr.remap.single.fq.gz
However, the files 6.add.bam.rechr.remap.fq1.gz and 6.add.bam.rechr.remap.fq2.gz are empty.
Could someone help me understand why these files are empty and how to resolve this issue?
Thank you in advance for your assistance!