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ERROR: Unable to find trf

Hi,
I am trying to run kneaddata on bash but I got the following error, although TRF is optional:
ERROR: Unable to find trf. Please provide the full path to trf with --trf.
These are the steps I followed:
1-I installed kneaddata using:
pip install --user kneaddata
2-I created a database for host:
kneaddata_database --download mouse_C57BL bowtie2 $DIR
3-I downloaded Trimmomatic binary (because I got a separate error asking me to provide path to Trimmomatic.jar)
4-Run kneaddata:
kneaddata --input $DIR/1-meta-sw2_S1_L001_R1_001.fastq --reference-db $DIR/mouse_C57BL_6NJ --trimmomatic $DIR/Trimmomatic-0.39/ --output kneaddataOutputSingleEnd

Thanks!
Wael

Hello Wael, Thank you for the detailed post! Sorry for any confusion but with the latest release of Kneaddata trf is now run by default. If you would install trf it should resolve the error you are seeing. Alternatively you can run with the option --bypass-trf to skip the trf section of the Kneaddata workflow.

Thank you,
Lauren

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