# ERROR kneaddata output files

**URL:** <https://forum.biobakery.org/t/error-kneaddata-output-files/6638>\
**Category:** KneadData\
**Created:** [February 12, 2024, 8:28pm UTC](https://forum.biobakery.org/t/error-kneaddata-output-files/6638 "2024-02-12T20:28:42Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Enkabloza](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/enkabloza/32/2732_2.png) [@Enkabloza](https://forum.biobakery.org/u/Enkabloza)\
**Post date:** [February 12, 2024, 8:28pm UTC](https://forum.biobakery.org/t/error-kneaddata-output-files/6638/1 "2024-02-12T20:28:42Z")

</div>

Hi!!  
I am trying to run kneadData on bash but I got the following output files after processing my raw files (3158\_R1.fastq.gz and 3158\_R2.fastq.gz) ) on Paired-End-Run mode:

Output files obtained:  
-reformatted\_identifiers5J47Ei\_decompressed\_1J7Skd\_SRR19109032\_pass\_2 SRR19109032\_pass\_1\_kneaddata.log  
-reformatted\_identifiersqmnaMs\_decompressed\_7QYa6i\_SRR19109032\_pass\_1  
-SRR19109032\_pass\_1\_kneaddata.log

I would like to clarify that my data is raw and not have been trimmed, so the problem comes because I didn’t trim before using kneadData?

Script:

kneaddata --input /mnt/Micro/villafandata/SRR191090$line\_pass\_1.fastq.gz --input /mnt/Micro/villafandata/SRR191090$line\_pass\_2.fastq.gz --reference-db /mnt/BUNDLE\_38/GRCh38\_noalt\_as --output /mnt/Micro/kneaddata\_controles/$line --bypass-trim

Thanks for read me!!  
Best  
Isra