Please I have a question regarding ChIP-Seq data analysis using Galaxy platform! During the trimming step (using Trim Galore) for ChIP-Seq data, I got error message:
Fatal error: Exit code 1 () Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 207 AGATCGGAAGAGC 1000000 0.02 smallRNA 3 TGGAATTCTCGG 1000000 0.00 Nextera 2 CTGTCTCTTATA 1000000 0.00 Using Illumina adapter for trimming (count: 207). Second best hit was smallRNA (count: 3) gzip: stdout: Broken pipe Writing report to './input_1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: input_1.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.3 Cutadapt version: 1.13 Quality Phred score cutoff: 15 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 3 bp Minimum required sequence length before a sequence gets removed: 20 bp Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz >>> Now performing quality (cutoff 15) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed This is cutadapt 1.13 with Python 3.6.1 Command line parameters: -f fastq -e 0.1 -q 15 -O 3 -a AGATCGGAAGAGC input_1.fastq.gz 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... gzip: stdout: Broken pipe
please if you can help me solve it!
Thank you very much!