SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_8_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_8_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 526.12 s (18 us/read; 3.38 M reads/minute). === Summary === Total reads processed: 29,619,538 Reads with adapters: 14,917,969 (50.4%) Reads written (passing filters): 29,619,538 (100.0%) Total basepairs processed: 2,260,916,887 bp Quality-trimmed: 2,375,264 bp (0.1%) Total written (filtered): 2,240,385,329 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14917969 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.7% C: 12.0% G: 10.9% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12734623 7404884.5 0 12734623 2 1654721 1851221.1 0 1654721 3 418088 462805.3 0 418088 4 64100 115701.3 0 64100 5 4898 28925.3 0 4898 6 4825 7231.3 0 4825 7 2422 1807.8 0 2422 8 1107 452.0 0 1107 9 929 113.0 0 268 661 10 1732 28.2 1 456 1276 11 1240 7.1 1 221 1019 12 1335 1.8 1 341 994 13 1850 0.4 1 0 1850 14 2618 0.4 1 0 2618 15 4918 0.4 1 0 4918 16 9233 0.4 1 0 9233 17 7451 0.4 1 0 7451 18 443 0.4 1 0 443 19 97 0.4 1 0 97 20 57 0.4 1 0 57 21 50 0.4 1 0 50 22 42 0.4 1 0 42 23 53 0.4 1 0 53 24 55 0.4 1 0 55 25 57 0.4 1 0 57 26 65 0.4 1 0 65 27 56 0.4 1 0 56 28 44 0.4 1 0 44 29 44 0.4 1 0 44 30 44 0.4 1 0 44 31 39 0.4 1 0 39 32 38 0.4 1 0 38 33 38 0.4 1 0 38 34 38 0.4 1 0 38 35 38 0.4 1 0 38 36 30 0.4 1 0 30 37 30 0.4 1 0 30 38 31 0.4 1 0 31 39 22 0.4 1 0 22 40 29 0.4 1 0 29 41 27 0.4 1 0 27 42 20 0.4 1 0 20 43 29 0.4 1 0 29 44 26 0.4 1 0 26 45 28 0.4 1 0 28 46 23 0.4 1 0 23 47 19 0.4 1 0 19 48 32 0.4 1 0 32 49 27 0.4 1 0 27 50 17 0.4 1 0 17 51 12 0.4 1 0 12 52 12 0.4 1 0 12 53 11 0.4 1 0 11 54 15 0.4 1 0 15 55 9 0.4 1 0 9 56 14 0.4 1 0 14 57 10 0.4 1 0 10 58 20 0.4 1 0 20 59 13 0.4 1 0 13 60 10 0.4 1 0 10 61 6 0.4 1 0 6 62 7 0.4 1 0 7 63 18 0.4 1 0 18 64 4 0.4 1 0 4 65 6 0.4 1 0 6 66 5 0.4 1 0 5 67 3 0.4 1 0 3 68 5 0.4 1 0 5 69 1 0.4 1 0 1 70 3 0.4 1 0 3 71 4 0.4 1 0 4 72 2 0.4 1 0 2 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_8_s1_R1_val_1.fq.gz ============================================= 29619538 sequences processed in total