SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_5_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_5_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 528.23 s (17 us/read; 3.59 M reads/minute). === Summary === Total reads processed: 31,629,718 Reads with adapters: 11,310,341 (35.8%) Reads written (passing filters): 31,629,718 (100.0%) Total basepairs processed: 2,408,754,938 bp Quality-trimmed: 1,286,497 bp (0.1%) Total written (filtered): 2,394,990,512 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11310341 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 13.8% G: 3.6% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10652114 7907429.5 0 10652114 2 466681 1976857.4 0 466681 3 137131 494214.3 0 137131 4 27002 123553.6 0 27002 5 2290 30888.4 0 2290 6 2170 7722.1 0 2170 7 466 1930.5 0 466 8 186 482.6 0 186 9 915 120.7 0 777 138 10 688 30.2 1 75 613 11 989 7.5 1 255 734 12 879 1.9 1 101 778 13 1466 0.5 1 0 1466 14 2820 0.5 1 0 2820 15 4385 0.5 1 0 4385 16 5573 0.5 1 0 5573 17 3358 0.5 1 0 3358 18 332 0.5 1 0 332 19 55 0.5 1 0 55 20 35 0.5 1 0 35 21 30 0.5 1 0 30 22 31 0.5 1 0 31 23 31 0.5 1 0 31 24 42 0.5 1 0 42 25 43 0.5 1 0 43 26 27 0.5 1 0 27 27 23 0.5 1 0 23 28 36 0.5 1 0 36 29 35 0.5 1 0 35 30 26 0.5 1 0 26 31 26 0.5 1 0 26 32 26 0.5 1 0 26 33 26 0.5 1 0 26 34 21 0.5 1 0 21 35 26 0.5 1 0 26 36 17 0.5 1 0 17 37 31 0.5 1 0 31 38 17 0.5 1 0 17 39 18 0.5 1 0 18 40 25 0.5 1 0 25 41 18 0.5 1 0 18 42 16 0.5 1 0 16 43 8 0.5 1 0 8 44 22 0.5 1 0 22 45 18 0.5 1 0 18 46 12 0.5 1 0 12 47 16 0.5 1 0 16 48 12 0.5 1 0 12 49 14 0.5 1 0 14 50 12 0.5 1 0 12 51 12 0.5 1 0 12 52 6 0.5 1 0 6 53 15 0.5 1 0 15 54 4 0.5 1 0 4 55 5 0.5 1 0 5 56 1 0.5 1 0 1 57 12 0.5 1 0 12 58 7 0.5 1 0 7 59 6 0.5 1 0 6 60 4 0.5 1 0 4 61 3 0.5 1 0 3 62 3 0.5 1 0 3 63 7 0.5 1 0 7 64 1 0.5 1 0 1 65 4 0.5 1 0 4 66 1 0.5 1 0 1 67 3 0.5 1 0 3 68 1 0.5 1 0 1 69 2 0.5 1 0 2 70 1 0.5 1 0 1 71 1 0.5 1 0 1 72 1 0.5 1 0 1 73 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_5_s1_R2_val_2.fq.gz ============================================= 31629718 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 31629718 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 84829 (0.27%)