SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_3_s1_R1_val_1.fq.gz Trimming mode: paired-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; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 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 ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18 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 zr2096_3_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 528.55 s (18 us/read; 3.37 M reads/minute). === Summary === Total reads processed: 29,717,035 Reads with adapters: 14,839,892 (49.9%) Reads written (passing filters): 29,717,035 (100.0%) Total basepairs processed: 2,250,213,060 bp Quality-trimmed: 2,201,183 bp (0.1%) Total written (filtered): 2,229,749,103 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14839892 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.5% C: 12.3% G: 11.2% T: 35.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12643021 7429258.8 0 12643021 2 1660557 1857314.7 0 1660557 3 416913 464328.7 0 416913 4 58121 116082.2 0 58121 5 4835 29020.5 0 4835 6 6188 7255.1 0 6188 7 2776 1813.8 0 2776 8 1330 453.4 0 1330 9 1563 113.4 0 393 1170 10 2379 28.3 1 708 1671 11 1616 7.1 1 335 1281 12 1802 1.8 1 402 1400 13 2639 0.4 1 0 2639 14 3753 0.4 1 0 3753 15 7039 0.4 1 0 7039 16 12740 0.4 1 0 12740 17 9851 0.4 1 0 9851 18 734 0.4 1 0 734 19 155 0.4 1 0 155 20 91 0.4 1 0 91 21 77 0.4 1 0 77 22 66 0.4 1 0 66 23 65 0.4 1 0 65 24 65 0.4 1 0 65 25 101 0.4 1 0 101 26 85 0.4 1 0 85 27 69 0.4 1 0 69 28 74 0.4 1 0 74 29 69 0.4 1 0 69 30 59 0.4 1 0 59 31 65 0.4 1 0 65 32 68 0.4 1 0 68 33 59 0.4 1 0 59 34 50 0.4 1 0 50 35 39 0.4 1 0 39 36 38 0.4 1 0 38 37 33 0.4 1 0 33 38 38 0.4 1 0 38 39 33 0.4 1 0 33 40 36 0.4 1 0 36 41 27 0.4 1 0 27 42 39 0.4 1 0 39 43 33 0.4 1 0 33 44 45 0.4 1 0 45 45 46 0.4 1 0 46 46 40 0.4 1 0 40 47 34 0.4 1 0 34 48 23 0.4 1 0 23 49 27 0.4 1 0 27 50 27 0.4 1 0 27 51 33 0.4 1 0 33 52 22 0.4 1 0 22 53 23 0.4 1 0 23 54 16 0.4 1 0 16 55 16 0.4 1 0 16 56 8 0.4 1 0 8 57 11 0.4 1 0 11 58 16 0.4 1 0 16 59 11 0.4 1 0 11 60 10 0.4 1 0 10 61 12 0.4 1 0 12 62 9 0.4 1 0 9 63 15 0.4 1 0 15 64 13 0.4 1 0 13 65 10 0.4 1 0 10 66 8 0.4 1 0 8 67 4 0.4 1 0 4 68 4 0.4 1 0 4 69 3 0.4 1 0 3 70 3 0.4 1 0 3 71 3 0.4 1 0 3 72 5 0.4 1 0 5 73 4 0.4 1 0 4 RUN STATISTICS FOR INPUT FILE: zr2096_3_s1_R1_val_1.fq.gz ============================================= 29717035 sequences processed in total