SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_10_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_10_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 295.53 s (17 us/read; 3.56 M reads/minute). === Summary === Total reads processed: 17,535,871 Reads with adapters: 6,542,882 (37.3%) Reads written (passing filters): 17,535,871 (100.0%) Total basepairs processed: 1,350,521,498 bp Quality-trimmed: 912,488 bp (0.1%) Total written (filtered): 1,342,409,660 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6542882 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.4% C: 13.3% G: 3.4% T: 35.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6191324 4383967.8 0 6191324 2 241739 1095991.9 0 241739 3 77178 273998.0 0 77178 4 15391 68499.5 0 15391 5 1837 17124.9 0 1837 6 1007 4281.2 0 1007 7 241 1070.3 0 241 8 131 267.6 0 131 9 645 66.9 0 536 109 10 421 16.7 1 45 376 11 857 4.2 1 212 645 12 557 1.0 1 69 488 13 1000 0.3 1 0 1000 14 1719 0.3 1 0 1719 15 2629 0.3 1 0 2629 16 3361 0.3 1 0 3361 17 2147 0.3 1 0 2147 18 185 0.3 1 0 185 19 36 0.3 1 0 36 20 19 0.3 1 0 19 21 20 0.3 1 0 20 22 25 0.3 1 0 25 23 20 0.3 1 0 20 24 25 0.3 1 0 25 25 25 0.3 1 0 25 26 17 0.3 1 0 17 27 15 0.3 1 0 15 28 29 0.3 1 0 29 29 15 0.3 1 0 15 30 18 0.3 1 0 18 31 24 0.3 1 0 24 32 14 0.3 1 0 14 33 7 0.3 1 0 7 34 10 0.3 1 0 10 35 8 0.3 1 0 8 36 6 0.3 1 0 6 37 6 0.3 1 0 6 38 2 0.3 1 0 2 39 12 0.3 1 0 12 40 12 0.3 1 0 12 41 10 0.3 1 0 10 42 9 0.3 1 0 9 43 11 0.3 1 0 11 44 9 0.3 1 0 9 45 15 0.3 1 0 15 46 10 0.3 1 0 10 47 6 0.3 1 0 6 48 8 0.3 1 0 8 49 8 0.3 1 0 8 50 8 0.3 1 0 8 51 9 0.3 1 0 9 52 3 0.3 1 0 3 53 4 0.3 1 0 4 54 3 0.3 1 0 3 55 3 0.3 1 0 3 56 3 0.3 1 0 3 57 4 0.3 1 0 4 58 2 0.3 1 0 2 59 3 0.3 1 0 3 60 3 0.3 1 0 3 61 3 0.3 1 0 3 62 1 0.3 1 0 1 63 1 0.3 1 0 1 64 3 0.3 1 0 3 65 1 0.3 1 0 1 66 1 0.3 1 0 1 68 2 0.3 1 0 2 69 1 0.3 1 0 1 70 1 0.3 1 0 1 72 1 0.3 1 0 1 73 1 0.3 1 0 1 74 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_10_s1_R2_val_2.fq.gz ============================================= 17535871 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17535871 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 69974 (0.40%)