SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_1_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_1_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 500.73 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 28,769,621 Reads with adapters: 13,951,269 (48.5%) Reads written (passing filters): 28,769,621 (100.0%) Total basepairs processed: 2,212,297,559 bp Quality-trimmed: 2,801,564 bp (0.1%) Total written (filtered): 2,192,471,144 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13951269 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.6% C: 12.9% G: 11.2% T: 33.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12089535 7192405.2 0 12089535 2 1366413 1798101.3 0 1366413 3 377788 449525.3 0 377788 4 51322 112381.3 0 51322 5 4482 28095.3 0 4482 6 10125 7023.8 0 10125 7 3455 1756.0 0 3455 8 1181 439.0 0 1181 9 903 109.7 0 371 532 10 2019 27.4 1 681 1338 11 1542 6.9 1 335 1207 12 2428 1.7 1 467 1961 13 2643 0.4 1 0 2643 14 3692 0.4 1 0 3692 15 7146 0.4 1 0 7146 16 12849 0.4 1 0 12849 17 10577 0.4 1 0 10577 18 787 0.4 1 0 787 19 185 0.4 1 0 185 20 80 0.4 1 0 80 21 78 0.4 1 0 78 22 76 0.4 1 0 76 23 96 0.4 1 0 96 24 110 0.4 1 0 110 25 116 0.4 1 0 116 26 112 0.4 1 0 112 27 98 0.4 1 0 98 28 82 0.4 1 0 82 29 66 0.4 1 0 66 30 97 0.4 1 0 97 31 78 0.4 1 0 78 32 63 0.4 1 0 63 33 64 0.4 1 0 64 34 72 0.4 1 0 72 35 61 0.4 1 0 61 36 48 0.4 1 0 48 37 56 0.4 1 0 56 38 62 0.4 1 0 62 39 48 0.4 1 0 48 40 43 0.4 1 0 43 41 44 0.4 1 0 44 42 39 0.4 1 0 39 43 23 0.4 1 0 23 44 37 0.4 1 0 37 45 36 0.4 1 0 36 46 29 0.4 1 0 29 47 35 0.4 1 0 35 48 34 0.4 1 0 34 49 23 0.4 1 0 23 50 28 0.4 1 0 28 51 25 0.4 1 0 25 52 27 0.4 1 0 27 53 25 0.4 1 0 25 54 18 0.4 1 0 18 55 14 0.4 1 0 14 56 18 0.4 1 0 18 57 16 0.4 1 0 16 58 15 0.4 1 0 15 59 9 0.4 1 0 9 60 8 0.4 1 0 8 61 11 0.4 1 0 11 62 10 0.4 1 0 10 63 10 0.4 1 0 10 64 11 0.4 1 0 11 65 6 0.4 1 0 6 66 10 0.4 1 0 10 67 9 0.4 1 0 9 68 6 0.4 1 0 6 69 4 0.4 1 0 4 70 5 0.4 1 0 5 71 4 0.4 1 0 4 72 1 0.4 1 0 1 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_1_s1_R1_val_1.fq.gz ============================================= 28769621 sequences processed in total