Question: Cutadapt terminated with exit signal: '24'.
0
gravatar for roy.granit
4 months ago by
roy.granit830
Israel/LabWorm
roy.granit830 wrote:

I'm using Trim Galore to process RNAseq and in one of the samples in get this error:

Cutadapt terminated with exit signal: '24'. Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

This is the code I've used:

../TrimGalore-0.6.4/trim_galore ./data/*fastq.gz -q 33 --nextera --path_to_cutadapt cutadapt --fastqc --fastqc_args "--nogroup --outdir ./fastqc_trimmed/" -o ./trimmed/

I could not find the meaning of the error in Cutadapt docs.. any ideas?

Thanks!

rna-seq • 162 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by roy.granit830

Please provide code. Did you check logs and error messages? This is a TrimGalore log message, not cutadapt.

ADD REPLYlink written 4 months ago by ATpoint36k

Trim Galore uses Cutadapt in the process, but nothing shows in the log :( just this

This is cutadapt 1.18 with Python 3.6.6 Command line parameters: -j 1 -e 0.1 -q 33 -O 1 -a CTGTCTCTTATA ./data/TCOC23_S14_R1_001.fastq.gz Processing reads on 1 core in single-end mode ...

Will add the code I've used to the original post

ADD REPLYlink written 4 months ago by roy.granit830

I would run cutadapt manually with these parameters and see where the problem is, so if it is indeed cutadapt or something else.

ADD REPLYlink written 4 months ago by ATpoint36k

Thanks, it ran OK with just cutadapt

ADD REPLYlink written 4 months ago by roy.granit830
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