SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_7_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_7_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 487.24 s (17 us/read; 3.62 M reads/minute). === Summary === Total reads processed: 29,396,171 Reads with adapters: 10,758,286 (36.6%) Reads written (passing filters): 29,396,171 (100.0%) Total basepairs processed: 2,277,104,260 bp Quality-trimmed: 1,105,332 bp (0.0%) Total written (filtered): 2,263,946,009 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10758286 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 13.7% G: 3.4% T: 36.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10149728 7349042.8 0 10149728 2 415524 1837260.7 0 415524 3 125897 459315.2 0 125897 4 25485 114828.8 0 25485 5 2188 28707.2 0 2188 6 2123 7176.8 0 2123 7 480 1794.2 0 480 8 239 448.5 0 239 9 1166 112.1 0 956 210 10 1018 28.0 1 117 901 11 1422 7.0 1 539 883 12 1403 1.8 1 183 1220 13 2531 0.4 1 0 2531 14 4759 0.4 1 0 4759 15 7190 0.4 1 0 7190 16 9467 0.4 1 0 9467 17 5914 0.4 1 0 5914 18 505 0.4 1 0 505 19 93 0.4 1 0 93 20 53 0.4 1 0 53 21 53 0.4 1 0 53 22 49 0.4 1 0 49 23 49 0.4 1 0 49 24 53 0.4 1 0 53 25 58 0.4 1 0 58 26 46 0.4 1 0 46 27 46 0.4 1 0 46 28 47 0.4 1 0 47 29 38 0.4 1 0 38 30 45 0.4 1 0 45 31 62 0.4 1 0 62 32 37 0.4 1 0 37 33 31 0.4 1 0 31 34 30 0.4 1 0 30 35 28 0.4 1 0 28 36 25 0.4 1 0 25 37 17 0.4 1 0 17 38 20 0.4 1 0 20 39 19 0.4 1 0 19 40 17 0.4 1 0 17 41 13 0.4 1 0 13 42 25 0.4 1 0 25 43 16 0.4 1 0 16 44 20 0.4 1 0 20 45 23 0.4 1 0 23 46 15 0.4 1 0 15 47 18 0.4 1 0 18 48 15 0.4 1 0 15 49 22 0.4 1 0 22 50 8 0.4 1 0 8 51 12 0.4 1 0 12 52 11 0.4 1 0 11 53 11 0.4 1 0 11 54 12 0.4 1 0 12 55 9 0.4 1 0 9 56 16 0.4 1 0 16 57 12 0.4 1 0 12 58 11 0.4 1 0 11 59 10 0.4 1 0 10 60 7 0.4 1 0 7 61 6 0.4 1 0 6 62 3 0.4 1 0 3 63 7 0.4 1 0 7 64 9 0.4 1 0 9 65 3 0.4 1 0 3 66 1 0.4 1 0 1 67 2 0.4 1 0 2 68 3 0.4 1 0 3 69 1 0.4 1 0 1 71 3 0.4 1 0 3 72 3 0.4 1 0 3 73 2 0.4 1 0 2 74 1 0.4 1 0 1 75 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_7_s1_R2_val_2.fq.gz ============================================= 29396171 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29396171 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 85493 (0.29%)