Kneaddata trf error

Hi,

I am having an issue with trf when running kneaddata. It only happens with this one sample (a negative sequencing control, the true samples all run without any issues).
The error in the log file isn’t particularly informative so I’m mostly hoping that somebody else has a trf issues and knows a fix.
The error and command used are below (with the command, the input is a tsv file with one sample per row where I’m pulling the sample name and paths to fwd and rev reads).

Thanks in advance,
Calum

while read sample read1 read2
do
    kneaddata \
        -i $read1 \
        -i $read2 \
        -o Kneaddata_Out/ \
        --output-prefix $sample \
        -db /home/cwwalsh/Databases/Kneaddata_HostRemoval/hg37dec_v0.1 \
        --trimmomatic /home/cwwalsh/miniconda3/envs/kneaddata/share/trimmomatic \
        -p 1 \
        -t 50 \
done < paths.tsv

05/19/2022 03:37:35 PM - kneaddata.utilities - CRITICAL: Error executing: kneaddata_trf_parallel --input /home/mdu/damg/analyses/CSF_Illumina_20220519/Kneaddata_Out/NTC-M2022-01733-M2022-01842.trimmed.single.1.fasta --output /home/mdu/damg/analyses/CSF_Illumina_20220519/Kneaddata_Out/NTC-M2022-01733-M2022-01842.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/cwwalsh/miniconda3/envs/kneaddata/bin/trf --trf-options ‘2 7 7 80 10 50 500 -h -ngs’ --nproc 50

I’ve also had a similar error with an extremely small sample in the past, here is the log :

Error executing: kneaddata_trf_parallel --input /localscratch/ronj2303.7200303.0/S-21-POLPIL-G/S-21-POLPIL-G.trimmed.single.1.fasta --output /localscratch/ronj2303.7200303.0/S-21-POLPIL-G/S-21-POLPIL-G.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /cvmfs/soft.mugqic/CentOS6/software/TRF/TRF-4.09/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 23

I suspect it happens when no trf is found but I have not tested that.

1 Like

Thanks @jorondo1 - good to know I’m not the only one running into this. Will continue without trf for the moment and come back to it.