Je-Demultiplex outputs not working in alignment stage

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Hi,

I have issues with aligning my FastQ files using BWA-MEM, once I have processed them with Je-Demultiplex. If I align the raw files I do not have any issues. I get the error listed below:

[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[mem_sam_pe] paired reads have different names: “M04360:104:000000000-JLK3L:1:1101:10306:1399:1:N:0:NCCAAT:CATGCATG”, "M04360:104:000000000-JLK3L:1:1101:10306:1399:2:N:0:NCCAAT:CATGCATG

Any suggestions on how to solve this issue?

Thanks.