SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_7_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_7_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 522.24 s (18 us/read; 3.38 M reads/minute). === Summary === Total reads processed: 29,396,171 Reads with adapters: 15,322,123 (52.1%) Reads written (passing filters): 29,396,171 (100.0%) Total basepairs processed: 2,268,807,805 bp Quality-trimmed: 2,405,652 bp (0.1%) Total written (filtered): 2,247,866,315 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15322123 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.3% C: 11.6% G: 10.4% T: 36.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13174202 7349042.8 0 13174202 2 1613069 1837260.7 0 1613069 3 425181 459315.2 0 425181 4 62087 114828.8 0 62087 5 5314 28707.2 0 5314 6 5442 7176.8 0 5442 7 2228 1794.2 0 2228 8 984 448.5 0 984 9 1235 112.1 0 317 918 10 1797 28.0 1 515 1282 11 1428 7.0 1 242 1186 12 1333 1.8 1 315 1018 13 1950 0.4 1 0 1950 14 2578 0.4 1 0 2578 15 4886 0.4 1 0 4886 16 8947 0.4 1 0 8947 17 7389 0.4 1 0 7389 18 518 0.4 1 0 518 19 92 0.4 1 0 92 20 71 0.4 1 0 71 21 42 0.4 1 0 42 22 61 0.4 1 0 61 23 65 0.4 1 0 65 24 54 0.4 1 0 54 25 62 0.4 1 0 62 26 65 0.4 1 0 65 27 37 0.4 1 0 37 28 40 0.4 1 0 40 29 31 0.4 1 0 31 30 35 0.4 1 0 35 31 50 0.4 1 0 50 32 46 0.4 1 0 46 33 39 0.4 1 0 39 34 48 0.4 1 0 48 35 40 0.4 1 0 40 36 36 0.4 1 0 36 37 35 0.4 1 0 35 38 33 0.4 1 0 33 39 30 0.4 1 0 30 40 35 0.4 1 0 35 41 24 0.4 1 0 24 42 25 0.4 1 0 25 43 28 0.4 1 0 28 44 24 0.4 1 0 24 45 36 0.4 1 0 36 46 31 0.4 1 0 31 47 33 0.4 1 0 33 48 18 0.4 1 0 18 49 23 0.4 1 0 23 50 27 0.4 1 0 27 51 24 0.4 1 0 24 52 21 0.4 1 0 21 53 22 0.4 1 0 22 54 9 0.4 1 0 9 55 23 0.4 1 0 23 56 20 0.4 1 0 20 57 16 0.4 1 0 16 58 15 0.4 1 0 15 59 8 0.4 1 0 8 60 11 0.4 1 0 11 61 14 0.4 1 0 14 62 4 0.4 1 0 4 63 13 0.4 1 0 13 64 6 0.4 1 0 6 65 6 0.4 1 0 6 66 3 0.4 1 0 3 67 5 0.4 1 0 5 68 3 0.4 1 0 3 69 6 0.4 1 0 6 70 2 0.4 1 0 2 71 3 0.4 1 0 3 72 4 0.4 1 0 4 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_7_s1_R1_val_1.fq.gz ============================================= 29396171 sequences processed in total