SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_1_s1_R2_val_2.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_1_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 480.94 s (17 us/read; 3.59 M reads/minute). === Summary === Total reads processed: 28,769,621 Reads with adapters: 10,183,601 (35.4%) Reads written (passing filters): 28,769,621 (100.0%) Total basepairs processed: 2,217,133,462 bp Quality-trimmed: 1,521,478 bp (0.1%) Total written (filtered): 2,204,094,879 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10183601 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.2% C: 14.7% G: 3.1% T: 33.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9628778 7192405.2 0 9628778 2 380148 1798101.3 0 380148 3 102398 449525.3 0 102398 4 19858 112381.3 0 19858 5 2661 28095.3 0 2661 6 3026 7023.8 0 3026 7 510 1756.0 0 510 8 316 439.0 0 316 9 1755 109.7 0 1284 471 10 1357 27.4 1 209 1148 11 1730 6.9 1 583 1147 12 1831 1.7 1 285 1546 13 3378 0.4 1 0 3378 14 6036 0.4 1 0 6036 15 9260 0.4 1 0 9260 16 11525 0.4 1 0 11525 17 6626 0.4 1 0 6626 18 634 0.4 1 0 634 19 133 0.4 1 0 133 20 81 0.4 1 0 81 21 52 0.4 1 0 52 22 88 0.4 1 0 88 23 74 0.4 1 0 74 24 96 0.4 1 0 96 25 104 0.4 1 0 104 26 86 0.4 1 0 86 27 72 0.4 1 0 72 28 66 0.4 1 0 66 29 70 0.4 1 0 70 30 58 0.4 1 0 58 31 57 0.4 1 0 57 32 56 0.4 1 0 56 33 61 0.4 1 0 61 34 39 0.4 1 0 39 35 25 0.4 1 0 25 36 39 0.4 1 0 39 37 29 0.4 1 0 29 38 24 0.4 1 0 24 39 35 0.4 1 0 35 40 22 0.4 1 0 22 41 40 0.4 1 0 40 42 28 0.4 1 0 28 43 24 0.4 1 0 24 44 28 0.4 1 0 28 45 22 0.4 1 0 22 46 25 0.4 1 0 25 47 16 0.4 1 0 16 48 17 0.4 1 0 17 49 10 0.4 1 0 10 50 19 0.4 1 0 19 51 10 0.4 1 0 10 52 14 0.4 1 0 14 53 19 0.4 1 0 19 54 17 0.4 1 0 17 55 12 0.4 1 0 12 56 10 0.4 1 0 10 57 8 0.4 1 0 8 58 6 0.4 1 0 6 59 6 0.4 1 0 6 60 8 0.4 1 0 8 61 8 0.4 1 0 8 62 12 0.4 1 0 12 63 5 0.4 1 0 5 64 5 0.4 1 0 5 65 3 0.4 1 0 3 66 6 0.4 1 0 6 67 6 0.4 1 0 6 68 5 0.4 1 0 5 69 5 0.4 1 0 5 70 5 0.4 1 0 5 71 3 0.4 1 0 3 72 3 0.4 1 0 3 74 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_1_s1_R2_val_2.fq.gz ============================================= 28769621 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 28769621 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 116452 (0.40%)