SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_10_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_10_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 317.85 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 17,535,871 Reads with adapters: 9,111,482 (52.0%) Reads written (passing filters): 17,535,871 (100.0%) Total basepairs processed: 1,343,649,791 bp Quality-trimmed: 2,371,417 bp (0.2%) Total written (filtered): 1,330,382,298 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9111482 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.8% C: 11.4% G: 10.5% T: 36.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7880131 4383967.8 0 7880131 2 916137 1095991.9 0 916137 3 254812 273998.0 0 254812 4 37063 68499.5 0 37063 5 4077 17124.9 0 4077 6 3562 4281.2 0 3562 7 985 1070.3 0 985 8 459 267.6 0 459 9 691 66.9 0 233 458 10 969 16.7 1 224 745 11 1142 4.2 1 141 1001 12 585 1.0 1 118 467 13 696 0.3 1 0 696 14 1021 0.3 1 0 1021 15 1963 0.3 1 0 1963 16 3493 0.3 1 0 3493 17 2845 0.3 1 0 2845 18 175 0.3 1 0 175 19 51 0.3 1 0 51 20 27 0.3 1 0 27 21 31 0.3 1 0 31 22 27 0.3 1 0 27 23 25 0.3 1 0 25 24 21 0.3 1 0 21 25 32 0.3 1 0 32 26 28 0.3 1 0 28 27 18 0.3 1 0 18 28 27 0.3 1 0 27 29 16 0.3 1 0 16 30 21 0.3 1 0 21 31 27 0.3 1 0 27 32 16 0.3 1 0 16 33 18 0.3 1 0 18 34 12 0.3 1 0 12 35 16 0.3 1 0 16 36 13 0.3 1 0 13 37 14 0.3 1 0 14 38 15 0.3 1 0 15 39 11 0.3 1 0 11 40 9 0.3 1 0 9 41 19 0.3 1 0 19 42 14 0.3 1 0 14 43 8 0.3 1 0 8 44 14 0.3 1 0 14 45 9 0.3 1 0 9 46 7 0.3 1 0 7 47 13 0.3 1 0 13 48 13 0.3 1 0 13 49 10 0.3 1 0 10 50 13 0.3 1 0 13 51 11 0.3 1 0 11 52 9 0.3 1 0 9 53 9 0.3 1 0 9 54 9 0.3 1 0 9 55 3 0.3 1 0 3 56 6 0.3 1 0 6 57 2 0.3 1 0 2 58 4 0.3 1 0 4 59 4 0.3 1 0 4 60 2 0.3 1 0 2 61 5 0.3 1 0 5 62 4 0.3 1 0 4 63 3 0.3 1 0 3 64 3 0.3 1 0 3 65 2 0.3 1 0 2 66 2 0.3 1 0 2 67 1 0.3 1 0 1 68 1 0.3 1 0 1 70 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_10_s1_R1_val_1.fq.gz ============================================= 17535871 sequences processed in total