extremly low properply paired rate using bowtie2

Question

[ljj_2016]

I used the following command for bowtie2 mapping (paired-end):

bowtie2 -p 6 -X 2000 --very-sensitive -x h38 -1 R1.trim.fq.gz -2 R2.trim.fq.gz |samtools sort -@ 5 -o sample1.bam 1>sample1.log 2>&1

The result was quite strange, with extremely low properly paired rate:

9881802 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
118700651 + 0 mapped (99.01% : N/A)
119881802 + 0 paired in sequencing
59940901 + 0 read1
59940901 + 0 read2
15941332 + 0 properly paired (13.30% : N/A)
118614966 + 0 with itself and mate mapped
85685 + 0 singletons (0.07% : N/A)
3806320 + 0 with mate mapped to a different chr
301236 + 0 with mate mapped to a different chr (mapQ>=5)

I don't think there was something really wrong with my bowtie2 command, and I think it's more likely due to my sample data. But I just wonder what happened with my sample during sequencing? Can anyone explain this phenomenon?**

[GenoMax]

Did you trim these paired-end data files independently? If so the two files are probably out of sync. You should either trim them together or use repair.sh from BBMap suite to clean/re-sync the trim files.

[ATpoint]

Details please. Which kind of data is this?

[ljj_2016]

sorry, I forgot to mention that it was ATAC-seq

[ATpoint]

I typically get like 98% being pp after all filtering steps. How did you trim?