SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/Serine/wd/18-04-10/zr2096_5_s1_R2.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) cutadapt version 1.16 Copyright (C) 2010-2017 Marcel Martin cutadapt removes adapter sequences from high-throughput sequencing reads. Usage: cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq For paired-end reads: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard characters are supported. The reverse complement is *not* automatically searched. All reads from input.fastq will be written to output.fastq with the adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter sequences can be given (use further -a options), but only the best-matching adapter will be removed. Input may also be in FASTA format. Compressed input and output is supported and auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for standard input/output. Without the -o option, output is sent to standard output. Citation: Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011. http://dx.doi.org/10.14806/ej.17.1.200 Use "cutadapt --help" to see all command-line options. See http://cutadapt.readthedocs.io/ for full documentation. cutadapt: error: [Errno 2] No such file or directory: '/Volumes/Serine/wd/18-04-10/zr2096_5_s1_R2.fastq'