SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_3_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_3_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 496.55 s (17 us/read; 3.59 M reads/minute). === Summary === Total reads processed: 29,717,035 Reads with adapters: 10,542,555 (35.5%) Reads written (passing filters): 29,717,035 (100.0%) Total basepairs processed: 2,255,215,984 bp Quality-trimmed: 1,235,022 bp (0.1%) Total written (filtered): 2,241,832,027 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10542555 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 14.2% G: 3.9% T: 36.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9855419 7429258.8 0 9855419 2 463577 1857314.7 0 463577 3 138213 464328.7 0 138213 4 25485 116082.2 0 25485 5 2509 29020.5 0 2509 6 2493 7255.1 0 2493 7 651 1813.8 0 651 8 331 453.4 0 331 9 1829 113.4 0 1488 341 10 1617 28.3 1 217 1400 11 2230 7.1 1 796 1434 12 2140 1.8 1 323 1817 13 4051 0.4 1 0 4051 14 7268 0.4 1 0 7268 15 11032 0.4 1 0 11032 16 13856 0.4 1 0 13856 17 7626 0.4 1 0 7626 18 721 0.4 1 0 721 19 128 0.4 1 0 128 20 85 0.4 1 0 85 21 72 0.4 1 0 72 22 65 0.4 1 0 65 23 74 0.4 1 0 74 24 90 0.4 1 0 90 25 53 0.4 1 0 53 26 79 0.4 1 0 79 27 55 0.4 1 0 55 28 61 0.4 1 0 61 29 56 0.4 1 0 56 30 65 0.4 1 0 65 31 67 0.4 1 0 67 32 44 0.4 1 0 44 33 31 0.4 1 0 31 34 30 0.4 1 0 30 35 23 0.4 1 0 23 36 26 0.4 1 0 26 37 23 0.4 1 0 23 38 26 0.4 1 0 26 39 21 0.4 1 0 21 40 19 0.4 1 0 19 41 16 0.4 1 0 16 42 16 0.4 1 0 16 43 29 0.4 1 0 29 44 14 0.4 1 0 14 45 20 0.4 1 0 20 46 20 0.4 1 0 20 47 5 0.4 1 0 5 48 15 0.4 1 0 15 49 12 0.4 1 0 12 50 17 0.4 1 0 17 51 7 0.4 1 0 7 52 10 0.4 1 0 10 53 6 0.4 1 0 6 54 9 0.4 1 0 9 55 12 0.4 1 0 12 56 9 0.4 1 0 9 57 12 0.4 1 0 12 58 9 0.4 1 0 9 59 9 0.4 1 0 9 60 8 0.4 1 0 8 61 10 0.4 1 0 10 62 11 0.4 1 0 11 63 7 0.4 1 0 7 64 7 0.4 1 0 7 65 7 0.4 1 0 7 66 5 0.4 1 0 5 67 5 0.4 1 0 5 68 3 0.4 1 0 3 69 2 0.4 1 0 2 72 1 0.4 1 0 1 73 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_3_s1_R2_val_2.fq.gz ============================================= 29717035 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29717035 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 116679 (0.39%)