SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_13_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 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): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_13_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1223.51 s (19 us/read; 3.19 M reads/minute). === Summary === Total reads processed: 65,081,682 Reads with adapters: 25,664,309 (39.4%) Reads written (passing filters): 65,081,682 (100.0%) Total basepairs processed: 3,272,837,182 bp Quality-trimmed: 3,459,477 bp (0.1%) Total written (filtered): 3,242,234,024 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25664309 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.6% C: 10.8% G: 3.7% T: 38.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 24665742 16270420.5 0 24665742 2 643781 4067605.1 0 643781 3 280330 1016901.3 0 280330 4 58268 254225.3 0 58268 5 8366 63556.3 0 8366 6 798 15889.1 0 798 7 2561 3972.3 0 2561 8 1035 993.1 0 1035 9 508 248.3 0 36 472 10 1126 62.1 1 2 1124 11 347 15.5 1 36 311 12 174 3.9 1 1 173 13 64 1.0 1 0 64 14 56 1.0 1 0 56 15 81 1.0 1 0 81 16 200 1.0 1 0 200 17 428 1.0 1 0 428 18 365 1.0 1 0 365 19 29 1.0 1 0 29 20 6 1.0 1 0 6 21 1 1.0 1 0 1 22 1 1.0 1 0 1 23 6 1.0 1 0 6 24 6 1.0 1 0 6 25 3 1.0 1 0 3 26 5 1.0 1 0 5 27 6 1.0 1 0 6 28 1 1.0 1 0 1 29 2 1.0 1 0 2 30 2 1.0 1 0 2 31 1 1.0 1 0 1 32 4 1.0 1 0 4 33 1 1.0 1 0 1 34 2 1.0 1 0 2 35 1 1.0 1 0 1 36 2 1.0 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_13_s456.fastq.gz ============================================= 65081682 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 729132 (1.1%)