SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_4_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_4_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 417.84 s (17 us/read; 3.47 M reads/minute). === Summary === Total reads processed: 24,165,270 Reads with adapters: 11,921,202 (49.3%) Reads written (passing filters): 24,165,270 (100.0%) Total basepairs processed: 1,774,487,009 bp Quality-trimmed: 1,789,083 bp (0.1%) Total written (filtered): 1,757,760,454 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11921202 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 13.1% G: 11.6% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10000118 6041317.5 0 10000118 2 1454355 1510329.4 0 1454355 3 364623 377582.3 0 364623 4 47308 94395.6 0 47308 5 4199 23598.9 0 4199 6 4181 5899.7 0 4181 7 2065 1474.9 0 2065 8 1141 368.7 0 1141 9 1051 92.2 0 320 731 10 2190 23.0 1 754 1436 11 1658 5.8 1 353 1305 12 1643 1.4 1 373 1270 13 2312 0.4 1 0 2312 14 3590 0.4 1 0 3590 15 6778 0.4 1 0 6778 16 12199 0.4 1 0 12199 17 9365 0.4 1 0 9365 18 689 0.4 1 0 689 19 130 0.4 1 0 130 20 87 0.4 1 0 87 21 72 0.4 1 0 72 22 68 0.4 1 0 68 23 56 0.4 1 0 56 24 73 0.4 1 0 73 25 94 0.4 1 0 94 26 79 0.4 1 0 79 27 67 0.4 1 0 67 28 61 0.4 1 0 61 29 55 0.4 1 0 55 30 64 0.4 1 0 64 31 61 0.4 1 0 61 32 51 0.4 1 0 51 33 45 0.4 1 0 45 34 31 0.4 1 0 31 35 31 0.4 1 0 31 36 43 0.4 1 0 43 37 38 0.4 1 0 38 38 27 0.4 1 0 27 39 27 0.4 1 0 27 40 31 0.4 1 0 31 41 34 0.4 1 0 34 42 37 0.4 1 0 37 43 16 0.4 1 0 16 44 24 0.4 1 0 24 45 32 0.4 1 0 32 46 25 0.4 1 0 25 47 22 0.4 1 0 22 48 25 0.4 1 0 25 49 18 0.4 1 0 18 50 13 0.4 1 0 13 51 20 0.4 1 0 20 52 21 0.4 1 0 21 53 14 0.4 1 0 14 54 11 0.4 1 0 11 55 14 0.4 1 0 14 56 15 0.4 1 0 15 57 12 0.4 1 0 12 58 11 0.4 1 0 11 59 9 0.4 1 0 9 60 8 0.4 1 0 8 61 8 0.4 1 0 8 62 10 0.4 1 0 10 63 9 0.4 1 0 9 64 10 0.4 1 0 10 65 6 0.4 1 0 6 66 1 0.4 1 0 1 67 5 0.4 1 0 5 68 3 0.4 1 0 3 69 1 0.4 1 0 1 70 3 0.4 1 0 3 71 4 0.4 1 0 4 72 3 0.4 1 0 3 73 1 0.4 1 0 1 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_4_s1_R1_val_1.fq.gz ============================================= 24165270 sequences processed in total