SUMMARISING RUN PARAMETERS ========================== Input filename: MT_rep1_1_Ch6.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 9). Second best hit was smallRNA (count: 0) 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 for both reads before a sequence pair gets removed: 20 bp Removing Ns from the start and end of reads Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 2.1 with Python 3.4.3 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 --trim-n -a AGATCGGAAGAGC MT_rep1_1_Ch6.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 87.97 s (54 us/read; 1.11 M reads/minute). === Summary === Total reads processed: 1,624,613 Reads with adapters: 578,951 (35.6%) Reads written (passing filters): 1,624,613 (100.0%) Total basepairs processed: 164,085,913 bp Quality-trimmed: 4,900,627 bp (3.0%) Total written (filtered): 158,376,030 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 578951 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.5% C: 26.9% G: 17.5% T: 18.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 426985 406153.2 0 426985 2 109539 101538.3 0 109539 3 31375 25384.6 0 31375 4 8210 6346.1 0 8210 5 1918 1586.5 0 1918 6 211 396.6 0 211 7 49 99.2 0 49 8 12 24.8 0 12 9 77 6.2 0 11 66 10 74 1.5 1 4 70 11 28 0.4 1 0 28 12 7 0.1 1 1 6 13 6 0.0 1 0 6 14 3 0.0 1 0 3 15 15 0.0 1 0 15 16 4 0.0 1 0 4 18 3 0.0 1 1 2 19 3 0.0 1 0 3 20 1 0.0 1 0 1 21 6 0.0 1 0 6 22 5 0.0 1 0 5 23 9 0.0 1 0 9 24 1 0.0 1 0 1 25 4 0.0 1 0 4 26 4 0.0 1 0 4 27 5 0.0 1 0 5 28 11 0.0 1 0 11 29 15 0.0 1 0 15 30 11 0.0 1 2 9 31 7 0.0 1 0 7 32 5 0.0 1 1 4 33 12 0.0 1 1 11 34 11 0.0 1 0 11 35 27 0.0 1 1 26 36 29 0.0 1 0 29 37 3 0.0 1 0 3 38 6 0.0 1 0 6 39 2 0.0 1 1 1 40 22 0.0 1 0 22 41 8 0.0 1 1 7 42 23 0.0 1 0 23 43 6 0.0 1 0 6 44 2 0.0 1 0 2 45 3 0.0 1 0 3 46 4 0.0 1 0 4 47 8 0.0 1 0 8 48 8 0.0 1 0 8 49 4 0.0 1 0 4 50 9 0.0 1 0 9 51 5 0.0 1 1 4 52 4 0.0 1 1 3 53 3 0.0 1 0 3 54 6 0.0 1 0 6 55 4 0.0 1 1 3 56 2 0.0 1 0 2 57 7 0.0 1 0 7 58 2 0.0 1 0 2 59 5 0.0 1 0 5 60 3 0.0 1 0 3 61 3 0.0 1 0 3 62 6 0.0 1 0 6 63 9 0.0 1 1 8 64 12 0.0 1 0 12 66 1 0.0 1 0 1 67 1 0.0 1 0 1 68 5 0.0 1 1 4 69 1 0.0 1 0 1 70 2 0.0 1 1 1 71 2 0.0 1 0 2 72 6 0.0 1 0 6 73 8 0.0 1 0 8 74 10 0.0 1 0 10 75 1 0.0 1 0 1 77 1 0.0 1 0 1 78 1 0.0 1 0 1 79 2 0.0 1 0 2 80 3 0.0 1 0 3 81 5 0.0 1 0 5 83 4 0.0 1 0 4 84 3 0.0 1 0 3 87 3 0.0 1 0 3 88 1 0.0 1 0 1 89 1 0.0 1 0 1 90 1 0.0 1 0 1 91 2 0.0 1 0 2 92 2 0.0 1 0 2 93 1 0.0 1 0 1 94 1 0.0 1 0 1 95 3 0.0 1 0 3 96 1 0.0 1 0 1 97 2 0.0 1 0 2 98 12 0.0 1 0 12 99 2 0.0 1 0 2 101 2 0.0 1 0 2 RUN STATISTICS FOR INPUT FILE: MT_rep1_1_Ch6.fastq.gz ============================================= 1624613 sequences processed in total