Error message

 Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted.

analysis

The prompt is that there is no sorting or R1 and R2 are not paired. Manually sort and then run HIC Pro step by step

samtools sort -@ 10 -n -m 10G -T temp1 xxxR1.bam > xxxR1.sort.bam
samtools sort -@ 10 -n -m 10G -T temp2 xxxR2.bam > xxxR2.sort.bam
mv xxxR1.sort.bam xxxR1.bam
mv xxxR1.sort.bam xxxR1.bam

be careful

It cannot be sorted by chromosome position, because HIC Pro needs pairing relationship in processing HIC data, so BAMS of R1 and R2 need to be sorted by name

-M cannot be set too low. If the HIC sequencing depth is high, there will be too many sorting process files and cannot be merged

It is best to set – t because there is a lot of IO interaction at this time.

Finally, modify and name the ordered documents according to their original names.

It cannot be executed with nohup, because it will redirect characters in standard output to BAM, resulting in some strange errors. You can use screen.