Paired-end reads somehow counted twice?

Hi. I’m new in Bioinformatics and try to extract read counts from fastq files.

I compared my result with answer count matrix, and read counts are doubled.

(Left one is from the answer read count matrix, and right one is my result.)

I used these commands on ubuntu to get my result:

Could you please tell me what went wrong?

hisat2 -p 50 
-x [ENSEMBL refrence file] 
-1 [fastq file_1] 
-2 [fastq file_2] 
-S [output file name].sam

samtools sort -@ 8 -o [output file name].bam [input file name].sam

featureCounts -p -T 10 -a [GTF file] 
-o [output file name] 
[input file name].bam

I think I didn’t apply pair-end option in some commands but I couldn’t figure out which one.