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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
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Problem with cutadapt line1 #44

Closed ChristophKramer closed 5 years ago

ChristophKramer commented 5 years ago

Hello, I want to use TrimGalore owith a fastq file. This is the command I am using:

TrimGalore-0.5.0/trim_galore -q 25 --fastqc --small_rna --max_length 28 --length 17 --max_n 5 -o GSM1585389_Trim_QC/ GSM1585389.fastq

I get the following erroer message: "This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 25 -O 1 -a TGGAATTCTCGG GSM1585389.fastq Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... cutadapt: error: Line 1 in FASTQ file is expected to start with '@', but found '\n'

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

If I run cutadapt with the command : cutadapt -f fastq -e 0.1 -q 25 -O 1 -a TGGAATTCTCGG GSM1585389.fastq

it works just fine. Any Idea what I can do about this issue?

Greetings Christoph Kramer

ChristophKramer commented 5 years ago

Apparantly the last line of my fastq file was empty and cutadapt couldn't cope with that. I removed it manually and now it works just fine.

Pardon me for the inconvinience.

FelixKrueger commented 5 years ago

I'm glad this one sorted itself out.