SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_2_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_2_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 532.93 s (17 us/read; 3.44 M reads/minute). === Summary === Total reads processed: 30,577,202 Reads with adapters: 14,512,994 (47.5%) Reads written (passing filters): 30,577,202 (100.0%) Total basepairs processed: 2,204,631,142 bp Quality-trimmed: 2,199,144 bp (0.1%) Total written (filtered): 2,184,012,404 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14512994 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.6% C: 13.6% G: 12.5% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12090258 7644300.5 0 12090258 2 1838068 1911075.1 0 1838068 3 449466 477768.8 0 449466 4 55948 119442.2 0 55948 5 5611 29860.5 0 5611 6 6664 7465.1 0 6664 7 3531 1866.3 0 3531 8 1562 466.6 0 1562 9 1300 116.6 0 485 815 10 2850 29.2 1 987 1863 11 2115 7.3 1 390 1725 12 2366 1.8 1 604 1762 13 3473 0.5 1 0 3473 14 5213 0.5 1 0 5213 15 9651 0.5 1 0 9651 16 17434 0.5 1 0 17434 17 13784 0.5 1 0 13784 18 1000 0.5 1 0 1000 19 229 0.5 1 0 229 20 101 0.5 1 0 101 21 117 0.5 1 0 117 22 113 0.5 1 0 113 23 85 0.5 1 0 85 24 99 0.5 1 0 99 25 112 0.5 1 0 112 26 124 0.5 1 0 124 27 106 0.5 1 0 106 28 97 0.5 1 0 97 29 82 0.5 1 0 82 30 108 0.5 1 0 108 31 73 0.5 1 0 73 32 92 0.5 1 0 92 33 87 0.5 1 0 87 34 79 0.5 1 0 79 35 62 0.5 1 0 62 36 46 0.5 1 0 46 37 53 0.5 1 0 53 38 50 0.5 1 0 50 39 41 0.5 1 0 41 40 43 0.5 1 0 43 41 47 0.5 1 0 47 42 53 0.5 1 0 53 43 51 0.5 1 0 51 44 53 0.5 1 0 53 45 48 0.5 1 0 48 46 36 0.5 1 0 36 47 34 0.5 1 0 34 48 34 0.5 1 0 34 49 29 0.5 1 0 29 50 31 0.5 1 0 31 51 32 0.5 1 0 32 52 34 0.5 1 0 34 53 22 0.5 1 0 22 54 19 0.5 1 0 19 55 20 0.5 1 0 20 56 23 0.5 1 0 23 57 11 0.5 1 0 11 58 16 0.5 1 0 16 59 18 0.5 1 0 18 60 9 0.5 1 0 9 61 18 0.5 1 0 18 62 10 0.5 1 0 10 63 6 0.5 1 0 6 64 5 0.5 1 0 5 65 11 0.5 1 0 11 66 7 0.5 1 0 7 67 8 0.5 1 0 8 68 1 0.5 1 0 1 69 2 0.5 1 0 2 70 5 0.5 1 0 5 71 3 0.5 1 0 3 72 1 0.5 1 0 1 73 1 0.5 1 0 1 74 2 0.5 1 0 2 75 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_2_s1_R1_val_1.fq.gz ============================================= 30577202 sequences processed in total