SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_8_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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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_8_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 541.07 s (18 us/read; 3.30 M reads/minute). === Summary === Total reads processed: 29,761,837 Reads with adapters: 13,441,159 (45.2%) Reads written (passing filters): 29,761,837 (100.0%) Total basepairs processed: 2,707,315,822 bp Quality-trimmed: 8,285,086 bp (0.3%) Total written (filtered): 2,682,461,698 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13441159 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.8% C: 6.3% G: 22.4% T: 44.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11303071 7440459.2 0 11303071 2 1459012 1860114.8 0 1459012 3 547133 465028.7 0 547133 4 82671 116257.2 0 82671 5 31711 29064.3 0 31711 6 10548 7266.1 0 10548 7 4205 1816.5 0 4205 8 81 454.1 0 81 9 68 113.5 0 6 62 10 113 28.4 1 1 112 11 73 7.1 1 0 73 12 40 1.8 1 0 40 13 42 1.8 1 0 42 14 60 1.8 1 0 60 15 25 1.8 1 0 25 16 31 1.8 1 0 31 17 29 1.8 1 0 29 18 41 1.8 1 1 40 19 25 1.8 1 0 25 20 29 1.8 1 0 29 21 31 1.8 1 0 31 22 41 1.8 1 0 41 23 41 1.8 1 0 41 24 34 1.8 1 0 34 25 35 1.8 1 0 35 26 43 1.8 1 1 42 27 33 1.8 1 0 33 28 34 1.8 1 0 34 29 27 1.8 1 0 27 30 44 1.8 1 0 44 31 33 1.8 1 0 33 32 34 1.8 1 1 33 33 38 1.8 1 1 37 34 41 1.8 1 0 41 35 38 1.8 1 0 38 36 26 1.8 1 0 26 37 36 1.8 1 0 36 38 31 1.8 1 0 31 39 42 1.8 1 0 42 40 39 1.8 1 0 39 41 27 1.8 1 0 27 42 44 1.8 1 0 44 43 31 1.8 1 0 31 44 25 1.8 1 0 25 45 47 1.8 1 0 47 46 32 1.8 1 0 32 47 30 1.8 1 0 30 48 32 1.8 1 0 32 49 31 1.8 1 0 31 50 29 1.8 1 1 28 51 40 1.8 1 0 40 52 22 1.8 1 0 22 53 20 1.8 1 0 20 54 32 1.8 1 0 32 55 31 1.8 1 0 31 56 35 1.8 1 0 35 57 27 1.8 1 0 27 58 29 1.8 1 0 29 59 26 1.8 1 2 24 60 38 1.8 1 1 37 61 16 1.8 1 0 16 62 34 1.8 1 0 34 63 18 1.8 1 0 18 64 23 1.8 1 0 23 65 31 1.8 1 0 31 66 19 1.8 1 0 19 67 19 1.8 1 0 19 68 18 1.8 1 0 18 69 18 1.8 1 1 17 70 28 1.8 1 0 28 71 32 1.8 1 0 32 72 28 1.8 1 0 28 73 22 1.8 1 0 22 74 26 1.8 1 0 26 75 16 1.8 1 0 16 76 24 1.8 1 0 24 77 26 1.8 1 0 26 78 13 1.8 1 0 13 79 38 1.8 1 1 37 80 14 1.8 1 0 14 81 17 1.8 1 0 17 82 23 1.8 1 0 23 83 21 1.8 1 0 21 84 22 1.8 1 0 22 85 21 1.8 1 0 21 86 21 1.8 1 0 21 87 21 1.8 1 0 21 88 19 1.8 1 0 19 89 21 1.8 1 0 21 90 19 1.8 1 0 19 91 16 1.8 1 0 16 92 24 1.8 1 0 24 93 13 1.8 1 0 13 94 22 1.8 1 0 22 95 12 1.8 1 0 12 96 10 1.8 1 0 10 97 16 1.8 1 0 16 98 13 1.8 1 0 13 99 8 1.8 1 0 8 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_8_s1_R1.fastq.gz ============================================= 29761837 sequences processed in total