ERROR: Unable to find trf

Infrastructure and utilities KneadData
1

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

2

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

1 Like
3

Hello, i ran into the same problem, could you tell me how to install the trf please?

5

https://anaconda.org/bioconda/trf

6

How to do it inside biobakery workflows? and if I want to use trf?

7

I was able to get trf to run by telling kneaddata the path to trf. Try putting --trf $Path to trf in your command

trf should be in your bin folder within your environment for kneaddata. I did not have to download trf separately.

e.g.
kneaddata --input1 sample.r1.fastq --input2 sample.r2.fastq -t 24 -db $MYENV/share/databases/human --trf $MYENV/bin --cat-final-output --output ./