# Kneaddata paired output have different names

**URL:** <https://forum.biobakery.org/t/kneaddata-paired-output-have-different-names/7454>\
**Category:** KneadData\
**Created:** [September 19, 2024, 4:43am UTC](https://forum.biobakery.org/t/kneaddata-paired-output-have-different-names/7454 "2024-09-19T04:43:25Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![guo](https://avatars.discourse-cdn.com/v4/letter/g/3ec8ea/32.png) [@guo](https://forum.biobakery.org/u/guo)\
**Post date:** [September 19, 2024, 4:43am UTC](https://forum.biobakery.org/t/kneaddata-paired-output-have-different-names/7454/1 "2024-09-19T04:43:25Z")

</div>

I have run kneaddata 0.12.0 on my metagenomics data. The data do not need to removed host-genome-contaminated reads, thus only use the trimmomatic options.  
kneaddata   
-i1 sample\_1.fq.gz   
-i2 sample\_2.fq.gz   
-o kneaddata -v -t 64   
–remove-intermediate-output   
–trimmomatic $PATH/soft/Trimmomatic-0.39/Trimmomatic-0.39/   
–trimmomatic-options ‘LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 AVGQUAL:20 MINLEN:50’  
I have \*\_1\_kneaddata.trimmed.1.fastq and \*\_1\_kneaddata.trimmed.2.fastq for each sample. But the title of reads do not put the paired-end symble “1” and “2” behind “#”, as the figure below.

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/c/ca35ae31f53a116dea656b70527ec23f0656dd15.jpeg)  
Then when I used metawrap binning, a wrong message was report as the below figure.  
 ![a604e82d4241c589397ebdcc8f7f268](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/7/72c9deeb68ef0680ff51e58bd56f8f97a1fa97f2.png)  
But when I used kneaddata v0.7.6 with the same code, the result is correct,the paired number 1 and 2 was behind #.  
 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/3/3ef849168b6a8bdf44229dd0e7ef618494c23bb0.jpeg)

How can I go about pairing these read correctly?

Thanks!