# Kneaddata paired reads?

**URL:** https://forum.biobakery.org/t/kneaddata-paired-reads/4503
**Category:** KneadData
**Created:** [December 8, 2022, 11:59am UTC](https://forum.biobakery.org/t/kneaddata-paired-reads/4503 "2022-12-08T11:59:21Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![reaset41](https://avatars.discourse-cdn.com/v4/letter/r/b5a626/32.png) [@reaset41](https://forum.biobakery.org/u/reaset41)
#### Post date: [December 8, 2022, 11:59am UTC](https://forum.biobakery.org/t/kneaddata-paired-reads/4503/1 "2022-12-08T11:59:21Z")

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I am using kneaddata v0.12.0 within a conda environment.

I am attempting to run kneaddata on paired-end reads. However, the output files are only for Read1. I am wondering whether kneaddata is not correctly identifying the paired read files.

kneaddata --input1 SRR689\_R1.fastq --input2 SRR689\_R2.fastq -db /Volumes/drive/hg\_bowtie --output kneaddata\_output/SRR689 --trimmomatic /Users/user/opt/anaconda3/envs/knead/share/trimmomatic-0.39-2 --sequencer-source NexteraPE