SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_6_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_6_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 454.30 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 24,237,290 Reads with adapters: 10,903,318 (45.0%) Reads written (passing filters): 24,237,290 (100.0%) Total basepairs processed: 2,142,776,317 bp Quality-trimmed: 6,660,811 bp (0.3%) Total written (filtered): 2,122,519,922 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 10903318 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.1% G: 23.4% T: 43.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9087937 6059322.5 0 9087937 2 1227972 1514830.6 0 1227972 3 467659 378707.7 0 467659 4 75619 94676.9 0 75619 5 30315 23669.2 0 30315 6 7702 5917.3 0 7702 7 3275 1479.3 0 3275 8 61 369.8 0 61 9 59 92.5 0 5 54 10 132 23.1 1 2 130 11 70 5.8 1 0 70 12 47 1.4 1 0 47 13 28 1.4 1 0 28 14 62 1.4 1 0 62 15 27 1.4 1 0 27 16 36 1.4 1 0 36 17 26 1.4 1 0 26 18 45 1.4 1 1 44 19 32 1.4 1 0 32 20 21 1.4 1 0 21 21 44 1.4 1 1 43 22 42 1.4 1 0 42 23 47 1.4 1 0 47 24 28 1.4 1 0 28 25 31 1.4 1 0 31 26 42 1.4 1 0 42 27 31 1.4 1 0 31 28 38 1.4 1 0 38 29 23 1.4 1 0 23 30 43 1.4 1 0 43 31 43 1.4 1 1 42 32 47 1.4 1 0 47 33 36 1.4 1 0 36 34 46 1.4 1 0 46 35 23 1.4 1 0 23 36 30 1.4 1 1 29 37 30 1.4 1 0 30 38 28 1.4 1 0 28 39 33 1.4 1 3 30 40 43 1.4 1 0 43 41 36 1.4 1 0 36 42 57 1.4 1 1 56 43 27 1.4 1 0 27 44 38 1.4 1 0 38 45 33 1.4 1 0 33 46 25 1.4 1 0 25 47 29 1.4 1 0 29 48 53 1.4 1 0 53 49 40 1.4 1 0 40 50 39 1.4 1 0 39 51 27 1.4 1 0 27 52 37 1.4 1 0 37 53 26 1.4 1 0 26 54 30 1.4 1 0 30 55 30 1.4 1 0 30 56 25 1.4 1 0 25 57 30 1.4 1 0 30 58 35 1.4 1 0 35 59 25 1.4 1 0 25 60 30 1.4 1 0 30 61 19 1.4 1 0 19 62 22 1.4 1 0 22 63 24 1.4 1 0 24 64 13 1.4 1 0 13 65 36 1.4 1 0 36 66 23 1.4 1 0 23 67 23 1.4 1 0 23 68 21 1.4 1 0 21 69 33 1.4 1 0 33 70 21 1.4 1 0 21 71 21 1.4 1 0 21 72 27 1.4 1 0 27 73 14 1.4 1 0 14 74 34 1.4 1 0 34 75 21 1.4 1 0 21 76 21 1.4 1 0 21 77 22 1.4 1 0 22 78 22 1.4 1 0 22 79 27 1.4 1 0 27 80 27 1.4 1 0 27 81 21 1.4 1 0 21 82 29 1.4 1 0 29 83 17 1.4 1 0 17 84 25 1.4 1 0 25 85 14 1.4 1 0 14 86 21 1.4 1 0 21 87 18 1.4 1 0 18 88 26 1.4 1 0 26 89 17 1.4 1 0 17 90 15 1.4 1 0 15 91 14 1.4 1 0 14 92 12 1.4 1 0 12 93 15 1.4 1 0 15 94 15 1.4 1 0 15 95 13 1.4 1 0 13 96 11 1.4 1 0 11 97 22 1.4 1 0 22 98 11 1.4 1 0 11 99 5 1.4 1 0 5 100 1 1.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_6_s1_R1.fastq.gz ============================================= 24237290 sequences processed in total