SUMMARISING RUN PARAMETERS ========================== Input filename: 6_GCCAAT_L001_R1_001.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 6_GCCAAT_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 233.41 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 12,489,766 Reads with adapters: 4,926,737 (39.4%) Reads written (passing filters): 12,489,766 (100.0%) Total basepairs processed: 636,978,066 bp Quality-trimmed: 2,185,070 bp (0.3%) Total written (filtered): 622,210,082 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4926737 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.5% C: 2.0% G: 21.7% T: 45.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3276852 3122441.5 0 3276852 2 794601 780610.4 0 794601 3 285283 195152.6 0 285283 4 128704 48788.1 0 128704 5 34517 12197.0 0 34517 6 30844 3049.3 0 30844 7 27794 762.3 0 27794 8 26986 190.6 0 26986 9 26705 47.6 0 26364 341 10 24540 11.9 1 23408 1132 11 22952 3.0 1 21953 999 12 22249 0.7 1 21427 822 13 19064 0.2 1 18363 701 14 20118 0.2 1 19165 953 15 18116 0.2 1 17196 920 16 17610 0.2 1 16786 824 17 15552 0.2 1 14920 632 18 14792 0.2 1 14184 608 19 13580 0.2 1 12901 679 20 13017 0.2 1 12408 609 21 12046 0.2 1 11420 626 22 11133 0.2 1 10543 590 23 10274 0.2 1 9720 554 24 9512 0.2 1 8930 582 25 8110 0.2 1 7681 429 26 7068 0.2 1 6648 420 27 6240 0.2 1 5852 388 28 5751 0.2 1 5401 350 29 5135 0.2 1 4807 328 30 3946 0.2 1 3711 235 31 2969 0.2 1 2764 205 32 2533 0.2 1 2391 142 33 1882 0.2 1 1783 99 34 1129 0.2 1 1075 54 35 677 0.2 1 633 44 36 417 0.2 1 393 24 37 181 0.2 1 171 10 38 147 0.2 1 140 7 39 94 0.2 1 87 7 40 78 0.2 1 73 5 41 108 0.2 1 97 11 42 189 0.2 1 173 16 43 214 0.2 1 201 13 44 419 0.2 1 390 29 45 541 0.2 1 524 17 46 683 0.2 1 649 34 47 542 0.2 1 494 48 48 110 0.2 1 96 14 49 49 0.2 1 37 12 50 61 0.2 1 59 2 51 623 0.2 1 514 109 RUN STATISTICS FOR INPUT FILE: 6_GCCAAT_L001_R1_001.fastq.gz ============================================= 12489766 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 314182 (2.5%)