SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_16_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_16_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1422.20 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 75,450,315 Reads with adapters: 29,474,701 (39.1%) Reads written (passing filters): 75,450,315 (100.0%) Total basepairs processed: 3,791,761,278 bp Quality-trimmed: 4,327,306 bp (0.1%) Total written (filtered): 3,756,311,075 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29474701 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.3% G: 3.7% T: 39.1% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 28373958 18862578.8 0 28373958 2 697695 4715644.7 0 697695 3 317779 1178911.2 0 317779 4 66050 294727.8 0 66050 5 10402 73681.9 0 10402 6 960 18420.5 0 960 7 2933 4605.1 0 2933 8 1094 1151.3 0 1094 9 602 287.8 0 66 536 10 1198 72.0 1 9 1189 11 374 18.0 1 39 335 12 182 4.5 1 1 181 13 69 1.1 1 0 69 14 71 1.1 1 0 71 15 90 1.1 1 0 90 16 235 1.1 1 0 235 17 515 1.1 1 0 515 18 381 1.1 1 0 381 19 42 1.1 1 0 42 20 12 1.1 1 0 12 21 4 1.1 1 0 4 22 4 1.1 1 0 4 23 1 1.1 1 0 1 24 5 1.1 1 0 5 25 4 1.1 1 0 4 26 3 1.1 1 0 3 27 13 1.1 1 0 13 28 2 1.1 1 0 2 29 9 1.1 1 0 9 30 2 1.1 1 0 2 31 4 1.1 1 0 4 32 4 1.1 1 0 4 33 1 1.1 1 0 1 34 1 1.1 1 0 1 35 1 1.1 1 0 1 36 1 1.1 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_16_s456.fastq.gz ============================================= 75450315 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 919259 (1.2%)