Hi
I try to run trim galore but received an error message (pasted below). It says "cutadapt ... failed at /usr/local/bin/trim_galore line 420". Anyone knows what it means?
thanks
###############################
$ No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
SUMMARISING RUN PARAMETERS
==========================
Input filename: Sample_C1.R1.fastq.gz
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG'
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 20 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: '--outdir ./'
Output file will be GZIP compressed
Writing final adapter and quality trimmed output to Sample_C1.R1_trimmed.fq
>>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG' from file Sample_C1.R1.fastq.gz <<<
open3: exec of cutadapt -f fastq -e 0.1 -q 20 -O 20 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG Sample_C1.R1.fastq.gz failed at /usr/local/bin/trim_galore line 420
RUN STATISTICS FOR INPUT FILE: Sample_C1.R1.fastq.gz
=============================================
0 sequences processed in total
Illegal division by zero at /usr/local/bin/trim_galore line 506.
^C
[3]- Exit 255 trim_galore --fastqc_args "--outdir ./" -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -s 20 Sample_C1.R1.fastq.gz
I try to run trim galore but received an error message (pasted below). It says "cutadapt ... failed at /usr/local/bin/trim_galore line 420". Anyone knows what it means?
thanks
###############################
$ No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
SUMMARISING RUN PARAMETERS
==========================
Input filename: Sample_C1.R1.fastq.gz
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG'
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 20 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: '--outdir ./'
Output file will be GZIP compressed
Writing final adapter and quality trimmed output to Sample_C1.R1_trimmed.fq
>>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG' from file Sample_C1.R1.fastq.gz <<<
open3: exec of cutadapt -f fastq -e 0.1 -q 20 -O 20 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG Sample_C1.R1.fastq.gz failed at /usr/local/bin/trim_galore line 420
RUN STATISTICS FOR INPUT FILE: Sample_C1.R1.fastq.gz
=============================================
0 sequences processed in total
Illegal division by zero at /usr/local/bin/trim_galore line 506.
^C
[3]- Exit 255 trim_galore --fastqc_args "--outdir ./" -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -s 20 Sample_C1.R1.fastq.gz
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