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?