Process reads_deduplication: issue with bam file in input to bamtofastq

A lot of warnings like these one are presents:

*****WARNING: Query J00173:56:HLHHYBBXX:6:1101:20324:2246 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

Test done : sort bam file and then bamtofastq on this sort file, same issue. samtools sort d.filtered.bam -o d.filtered.sort.bam samtools sort d.filtered.bam -n -o d.filtered.sort.new.bam