# KneadData unmatched paired reads

**URL:** <https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758>\
**Category:** KneadData\
**Created:** [February 5, 2026, 2:26pm UTC](https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758 "2026-02-05T14:26:50Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![stonescoding](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/stonescoding/32/3563_2.png) [@stonescoding](https://forum.biobakery.org/u/stonescoding)\
**Post date:** [February 5, 2026, 2:26pm UTC](https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758/1 "2026-02-05T14:26:50Z")

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Good afternoon, I am trying to run KneadData (version 0.12.0) on the iHMP IBD MTX dataset and on an IBS dataset. I noticed that paired reads that do not have the same read length end up in their respective unmatched fastq files. Hence, I end up with almost empty paired fastq files. As I would like to assemble contigs using rnaSPAdes, I would need more paired reads given that with the current KneadData output, rnaSPAdes fails for most samples. Is there a way to force KneadData to write unmatched paired reads into paired fastq files even if paired reads do not have the same read length?

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**Author:** ![stonescoding](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/stonescoding/32/3563_2.png) [@stonescoding](https://forum.biobakery.org/u/stonescoding)\
**Post date:** [February 9, 2026, 10:12am UTC](https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758/2 "2026-02-09T10:12:23Z")

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By further inspecting the raw reads fastq files and the KneadData outputs, I concluded that the read length is encoded in the reads’ headers, causing paired reads with different reads lengths to be considered as unmatched reads by KneadData. The solution would be to remove the reads lengths from the reads headers.

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**Author:** ![lfreund](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/lfreund/32/3046_2.png) [@lfreund](https://forum.biobakery.org/u/lfreund)\
**Post date:** [February 20, 2026, 9:34pm UTC](https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758/3 "2026-02-20T21:34:18Z")

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Hi there, I’ve been having this same issue and I think you’re correct, the read headers need to be changed for KneadData to work (i.e., I downloaded these sequence data from SRA and found this to be the case).

There are some solutions here: [All paired-end read unmatched - #21 by jorondo1](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/21)