SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_4_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_4_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 860.55 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 45,411,925 Reads with adapters: 18,217,042 (40.1%) Reads written (passing filters): 45,411,925 (100.0%) Total basepairs processed: 2,284,287,588 bp Quality-trimmed: 2,381,487 bp (0.1%) Total written (filtered): 2,262,602,788 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18217042 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.8% C: 10.7% G: 3.6% T: 38.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 17501301 11352981.2 0 17501301 2 455423 2838245.3 0 455423 3 205565 709561.3 0 205565 4 42473 177390.3 0 42473 5 5508 44347.6 0 5508 6 614 11086.9 0 614 7 1579 2771.7 0 1579 8 658 692.9 0 658 9 360 173.2 0 34 326 10 696 43.3 1 11 685 11 290 10.8 1 42 248 12 178 2.7 1 3 175 13 87 0.7 1 0 87 14 73 0.7 1 0 73 15 140 0.7 1 0 140 16 323 0.7 1 0 323 17 895 0.7 1 0 895 18 680 0.7 1 0 680 19 79 0.7 1 0 79 20 14 0.7 1 0 14 21 12 0.7 1 0 12 22 9 0.7 1 0 9 23 4 0.7 1 0 4 24 7 0.7 1 0 7 25 9 0.7 1 0 9 26 18 0.7 1 0 18 27 7 0.7 1 0 7 28 6 0.7 1 0 6 29 5 0.7 1 0 5 30 5 0.7 1 0 5 31 4 0.7 1 0 4 32 1 0.7 1 0 1 33 8 0.7 1 0 8 34 8 0.7 1 0 8 35 1 0.7 1 0 1 36 1 0.7 1 0 1 37 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_4_s456.fastq.gz ============================================= 45411925 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 506847 (1.1%)