# Je-Demultiplex outputs not working in alignment stage

**URL:** https://help.galaxyproject.org/t/je-demultiplex-outputs-not-working-in-alignment-stage/6690
**Category:** usegalaxy.org support
**Tags:** mapping, quality-control
**Created:** [September 16, 2021, 2:51pm UTC](https://help.galaxyproject.org/t/je-demultiplex-outputs-not-working-in-alignment-stage/6690 "2021-09-16T14:51:21Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![stauntok](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/stauntok/32/1898_2.png) [@stauntok](https://help.galaxyproject.org/u/stauntok)
#### Post date: [September 16, 2021, 2:51pm UTC](https://help.galaxyproject.org/t/je-demultiplex-outputs-not-working-in-alignment-stage/6690/1 "2021-09-16T14:51:21Z")

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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.

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### Author: ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [December 21, 2023, 10:57pm UTC](https://help.galaxyproject.org/t/je-demultiplex-outputs-not-working-in-alignment-stage/6690/2 "2023-12-21T22:57:38Z")

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