SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_4_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_4_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 397.43 s (16 us/read; 3.65 M reads/minute). === Summary === Total reads processed: 24,165,270 Reads with adapters: 8,490,982 (35.1%) Reads written (passing filters): 24,165,270 (100.0%) Total basepairs processed: 1,778,167,602 bp Quality-trimmed: 1,046,692 bp (0.1%) Total written (filtered): 1,767,000,593 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8490982 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 15.3% G: 4.1% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7857531 6041317.5 0 7857531 2 418598 1510329.4 0 418598 3 126135 377582.3 0 126135 4 21522 94395.6 0 21522 5 2047 23598.9 0 2047 6 2472 5899.7 0 2472 7 578 1474.9 0 578 8 347 368.7 0 347 9 2202 92.2 0 1819 383 10 1780 23.0 1 270 1510 11 2485 5.8 1 880 1605 12 2667 1.4 1 440 2227 13 4671 0.4 1 0 4671 14 8700 0.4 1 0 8700 15 13182 0.4 1 0 13182 16 15593 0.4 1 0 15593 17 7996 0.4 1 0 7996 18 843 0.4 1 0 843 19 175 0.4 1 0 175 20 90 0.4 1 0 90 21 79 0.4 1 0 79 22 69 0.4 1 0 69 23 78 0.4 1 0 78 24 76 0.4 1 0 76 25 81 0.4 1 0 81 26 66 0.4 1 0 66 27 74 0.4 1 0 74 28 58 0.4 1 0 58 29 54 0.4 1 0 54 30 63 0.4 1 0 63 31 46 0.4 1 0 46 32 57 0.4 1 0 57 33 44 0.4 1 0 44 34 41 0.4 1 0 41 35 26 0.4 1 0 26 36 28 0.4 1 0 28 37 28 0.4 1 0 28 38 26 0.4 1 0 26 39 18 0.4 1 0 18 40 31 0.4 1 0 31 41 25 0.4 1 0 25 42 23 0.4 1 0 23 43 24 0.4 1 0 24 44 16 0.4 1 0 16 45 16 0.4 1 0 16 46 18 0.4 1 0 18 47 15 0.4 1 0 15 48 13 0.4 1 0 13 49 7 0.4 1 0 7 50 17 0.4 1 0 17 51 14 0.4 1 0 14 52 9 0.4 1 0 9 53 10 0.4 1 0 10 54 12 0.4 1 0 12 55 13 0.4 1 0 13 56 5 0.4 1 0 5 57 9 0.4 1 0 9 58 7 0.4 1 0 7 59 6 0.4 1 0 6 60 11 0.4 1 0 11 61 11 0.4 1 0 11 62 4 0.4 1 0 4 63 4 0.4 1 0 4 64 8 0.4 1 0 8 65 1 0.4 1 0 1 66 6 0.4 1 0 6 67 3 0.4 1 0 3 68 5 0.4 1 0 5 69 5 0.4 1 0 5 70 1 0.4 1 0 1 71 4 0.4 1 0 4 72 3 0.4 1 0 3 RUN STATISTICS FOR INPUT FILE: zr2096_4_s1_R2_val_2.fq.gz ============================================= 24165270 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24165270 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134660 (0.56%)