SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_1_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_1_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 534.50 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 28,982,766 Reads with adapters: 12,553,900 (43.3%) Reads written (passing filters): 28,982,766 (100.0%) Total basepairs processed: 2,652,423,020 bp Quality-trimmed: 11,158,723 bp (0.4%) Total written (filtered): 2,625,957,959 bp (99.0%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 12553900 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 24.8% C: 6.4% G: 22.8% T: 45.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10658399 7245691.5 0 10658399 2 1276010 1811422.9 0 1276010 3 507213 452855.7 0 507213 4 75615 113213.9 0 75615 5 24781 28303.5 0 24781 6 7188 7075.9 0 7188 7 2888 1769.0 0 2888 8 30 442.2 0 30 9 26 110.6 0 7 19 10 90 27.6 1 0 90 11 44 6.9 1 0 44 12 26 1.7 1 0 26 13 24 1.7 1 0 24 14 23 1.7 1 0 23 15 21 1.7 1 0 21 16 22 1.7 1 0 22 17 24 1.7 1 0 24 18 25 1.7 1 0 25 19 18 1.7 1 0 18 20 13 1.7 1 0 13 21 19 1.7 1 0 19 22 19 1.7 1 0 19 23 23 1.7 1 0 23 24 13 1.7 1 0 13 25 22 1.7 1 0 22 26 27 1.7 1 0 27 27 12 1.7 1 0 12 28 24 1.7 1 0 24 29 16 1.7 1 0 16 30 36 1.7 1 0 36 31 18 1.7 1 0 18 32 21 1.7 1 0 21 33 14 1.7 1 0 14 34 24 1.7 1 0 24 35 24 1.7 1 0 24 36 25 1.7 1 0 25 37 23 1.7 1 0 23 38 25 1.7 1 0 25 39 15 1.7 1 0 15 40 19 1.7 1 0 19 41 21 1.7 1 0 21 42 30 1.7 1 0 30 43 20 1.7 1 0 20 44 29 1.7 1 0 29 45 16 1.7 1 0 16 46 24 1.7 1 0 24 47 14 1.7 1 0 14 48 21 1.7 1 0 21 49 23 1.7 1 0 23 50 15 1.7 1 0 15 51 28 1.7 1 0 28 52 16 1.7 1 0 16 53 18 1.7 1 0 18 54 21 1.7 1 0 21 55 19 1.7 1 0 19 56 16 1.7 1 0 16 57 24 1.7 1 0 24 58 13 1.7 1 0 13 59 19 1.7 1 1 18 60 19 1.7 1 0 19 61 18 1.7 1 0 18 62 25 1.7 1 1 24 63 12 1.7 1 0 12 64 18 1.7 1 0 18 65 21 1.7 1 0 21 66 15 1.7 1 0 15 67 24 1.7 1 0 24 68 8 1.7 1 0 8 69 18 1.7 1 0 18 70 19 1.7 1 0 19 71 18 1.7 1 0 18 72 18 1.7 1 0 18 73 23 1.7 1 0 23 74 15 1.7 1 0 15 75 14 1.7 1 0 14 76 12 1.7 1 0 12 77 20 1.7 1 0 20 78 12 1.7 1 0 12 79 15 1.7 1 0 15 80 18 1.7 1 0 18 81 21 1.7 1 0 21 82 15 1.7 1 0 15 83 21 1.7 1 0 21 84 11 1.7 1 0 11 85 11 1.7 1 0 11 86 14 1.7 1 0 14 87 23 1.7 1 0 23 88 15 1.7 1 0 15 89 12 1.7 1 0 12 90 9 1.7 1 0 9 91 12 1.7 1 0 12 92 12 1.7 1 0 12 93 9 1.7 1 0 9 94 11 1.7 1 0 11 95 12 1.7 1 0 12 96 9 1.7 1 0 9 97 13 1.7 1 0 13 98 11 1.7 1 0 11 99 7 1.7 1 0 7 100 4 1.7 1 0 4 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_1_s1_R1.fastq.gz ============================================= 28982766 sequences processed in total