Hello, I got .bam files from my pipeline and i merged them with samtools merge ALL.bam *.bam and I got this % of mapping

3825773 + 0 in total (QC-passed reads + QC-failed reads)
3825773 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
698306 + 0 mapped (18.25% : N/A)
698306 + 0 primary mapped (18.25% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5) 

I followed the advices from Can't convert paired end BAM to bed using bedtools and run

samtools sort -n ALL.bam > ALL.sorted.bam
samtools fixmate All.sorted.bam > ALL.fixed.bam
samtools sort ALL.fixed.bam > ALL.fixed.sorted
bedtools bamtobed -i ALL.fixed.sorted.bam -bedpe > ALL.bedpe

unfortunatelly, samtools flagstat ALL.fixed.bam showed me the same numbers and my ALL.bedpe is still empty

3825773 + 0 in total (QC-passed reads + QC-failed reads)
3825773 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
698283 + 0 mapped (18.25% : N/A)
698283 + 0 primary mapped (18.25% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Do you have any clues why it is like this?

Thank you, Best,