SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_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 /mnt/owl/nightingales/C_virginica/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 558.54 s (18 us/read; 3.31 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: /mnt/owl/nightingales/C_virginica/zr2096_2_s1_R1.fastq.gz ============================================= 30798582 sequences processed in total