SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.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: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 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/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_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 TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 560.17 s (18 us/read; 3.30 M reads/minute). === Summary === Total reads processed: 30,798,582 Reads with adapters: 13,311,629 (43.2%) Reads written (passing filters): 30,798,582 (100.0%) Total basepairs processed: 2,667,762,176 bp Quality-trimmed: 8,816,864 bp (0.3%) Total written (filtered): 2,642,064,564 bp (99.0%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13311629 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 25.0% C: 6.6% G: 25.5% T: 42.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10904738 7699645.5 0 10904738 2 1590759 1924911.4 0 1590759 3 664944 481227.8 0 664944 4 98584 120307.0 0 98584 5 35292 30076.7 0 35292 6 10391 7519.2 0 10391 7 3699 1879.8 0 3699 8 76 469.9 0 76 9 64 117.5 0 13 51 10 127 29.4 1 0 127 11 83 7.3 1 1 82 12 47 1.8 1 0 47 13 47 1.8 1 0 47 14 85 1.8 1 0 85 15 45 1.8 1 0 45 16 32 1.8 1 0 32 17 32 1.8 1 1 31 18 56 1.8 1 0 56 19 37 1.8 1 0 37 20 40 1.8 1 0 40 21 45 1.8 1 0 45 22 44 1.8 1 0 44 23 59 1.8 1 0 59 24 44 1.8 1 0 44 25 41 1.8 1 0 41 26 52 1.8 1 0 52 27 43 1.8 1 1 42 28 35 1.8 1 0 35 29 28 1.8 1 0 28 30 42 1.8 1 0 42 31 37 1.8 1 0 37 32 32 1.8 1 0 32 33 45 1.8 1 0 45 34 40 1.8 1 0 40 35 50 1.8 1 0 50 36 33 1.8 1 0 33 37 40 1.8 1 0 40 38 34 1.8 1 0 34 39 50 1.8 1 0 50 40 38 1.8 1 0 38 41 28 1.8 1 0 28 42 52 1.8 1 0 52 43 38 1.8 1 0 38 44 34 1.8 1 0 34 45 36 1.8 1 0 36 46 28 1.8 1 0 28 47 28 1.8 1 0 28 48 34 1.8 1 0 34 49 57 1.8 1 0 57 50 61 1.8 1 0 61 51 37 1.8 1 0 37 52 36 1.8 1 0 36 53 41 1.8 1 0 41 54 42 1.8 1 0 42 55 42 1.8 1 0 42 56 27 1.8 1 0 27 57 51 1.8 1 0 51 58 31 1.8 1 0 31 59 28 1.8 1 0 28 60 38 1.8 1 0 38 61 33 1.8 1 0 33 62 22 1.8 1 0 22 63 26 1.8 1 0 26 64 24 1.8 1 0 24 65 27 1.8 1 0 27 66 24 1.8 1 0 24 67 29 1.8 1 1 28 68 15 1.8 1 0 15 69 29 1.8 1 0 29 70 16 1.8 1 0 16 71 23 1.8 1 0 23 72 20 1.8 1 0 20 73 23 1.8 1 0 23 74 33 1.8 1 0 33 75 12 1.8 1 0 12 76 37 1.8 1 0 37 77 28 1.8 1 0 28 78 27 1.8 1 0 27 79 21 1.8 1 0 21 80 13 1.8 1 0 13 81 19 1.8 1 0 19 82 17 1.8 1 0 17 83 17 1.8 1 0 17 84 25 1.8 1 0 25 85 19 1.8 1 0 19 86 26 1.8 1 0 26 87 29 1.8 1 0 29 88 25 1.8 1 0 25 89 21 1.8 1 0 21 90 16 1.8 1 0 16 91 23 1.8 1 0 23 92 23 1.8 1 0 23 93 20 1.8 1 0 20 94 17 1.8 1 0 17 95 13 1.8 1 0 13 96 13 1.8 1 0 13 97 20 1.8 1 0 20 98 16 1.8 1 0 16 99 7 1.8 1 0 7 100 2 1.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.gz ============================================= 30798582 sequences processed in total