Question: Trim galore terminates with exit signal: '256'
0
gravatar for Sinji
2.5 years ago by
Sinji2.7k
UT Southwestern Medical Center
Sinji2.7k wrote:

I've built a very simple ChIP-seq pipeline using Nextflow, and it generally works. The problem I’m having is ... whenever I attempt to use trim_galore to pre-trim my Input data, I get an error. If I don't include my Input data, I get no error and the pipeline proceeds as it should.

I ran the following:

trim_galore --fastqc $input_file

And the following error is generated:

This is cutadapt 1.9.1 with Python 2.7.11
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Control.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
cutadapt: error: At line 3: Sequence descriptions in the FASTQ file don't match ('ROCKFORD:8:11:11825:13179#0/1' != 'ROCKFORD:8:11:f').
The second sequence description must be either empty or equal to the first description.

gzip: stdout: Broken pipe

Cutadapt terminated with exit signal: '256'.

The other two fastq files are trimmed fine. I'm not entirely sure what to do. I just received these files from the sequencing core so nothing has been done to them. Any thoughts?

cutadapt trim_galore • 2.0k views
ADD COMMENTlink modified 11 months ago by ZheFrench140 • written 2.5 years ago by Sinji2.7k

I got the same issue after a download on sra:

fastq-dump -split-3 SRR4235527

trim_galore --paired --fastqc --output_dir /GM12878/ SRR4235527_R1.fastq SRR4235527_R2.fastq

cutadapt: error: At line 3: Sequence descriptions in the FASTQ file don't match ('SRR4235527.43679310 TUPAC_0006:2:34:3219:8674 length=76' != 'SRR4235527.43679310 '). The second sequence description must be either empty or equal to the first description.

Cutadapt terminated with exit signal: '256'. Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

I have check files with :

vdb-validate SRR4235527

Nothing weird ... any idea ?

ADD REPLYlink written 11 months ago by ZheFrench140
1

Either re-fastq-dump the reads with -F option to recover original Illumina style fastq headers or get the fastq's from ENA.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax58k

Yeah this is what I did fastq's from ENA solution and it then worked fine. Thanks

ADD REPLYlink modified 11 months ago • written 11 months ago by ZheFrench140
2
gravatar for Devon Ryan
2.5 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

The error message is fairly clear. Ask the sequencing facility to regenerate the files and then double check that this is fixed before sending it back to you. They should also double check the other files they've produced lately for others.

ADD COMMENTlink written 2.5 years ago by Devon Ryan86k

Just wanted to make sure that this isn't a problem with my process. I'll have to go ahead and contact the sequencing core. Thanks!

ADD REPLYlink written 2.5 years ago by Sinji2.7k

To be fair to the facility you may have a copy that got corrupted during download. I would suggest giving download another try before contacting the facility. We have handled thousands of samples over the years and I don't recall having an issue like this.

ADD REPLYlink written 2.5 years ago by genomax58k
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