SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_5_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_5_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 586.07 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 31,778,715 Reads with adapters: 14,444,625 (45.5%) Reads written (passing filters): 31,778,715 (100.0%) Total basepairs processed: 2,881,909,346 bp Quality-trimmed: 9,171,799 bp (0.3%) Total written (filtered): 2,854,903,402 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 14444625 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.1% C: 6.0% G: 22.2% T: 44.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12146141 7944678.8 0 12146141 2 1572510 1986169.7 0 1572510 3 579698 496542.4 0 579698 4 91296 124135.6 0 91296 5 36238 31033.9 0 36238 6 10602 7758.5 0 10602 7 4501 1939.6 0 4501 8 92 484.9 0 92 9 78 121.2 0 15 63 10 162 30.3 1 0 162 11 104 7.6 1 0 104 12 42 1.9 1 0 42 13 62 1.9 1 0 62 14 71 1.9 1 1 70 15 41 1.9 1 0 41 16 40 1.9 1 0 40 17 37 1.9 1 0 37 18 45 1.9 1 0 45 19 28 1.9 1 0 28 20 32 1.9 1 0 32 21 37 1.9 1 0 37 22 48 1.9 1 0 48 23 50 1.9 1 0 50 24 53 1.9 1 0 53 25 40 1.9 1 1 39 26 70 1.9 1 1 69 27 59 1.9 1 0 59 28 34 1.9 1 0 34 29 46 1.9 1 0 46 30 49 1.9 1 0 49 31 38 1.9 1 0 38 32 38 1.9 1 0 38 33 42 1.9 1 0 42 34 44 1.9 1 0 44 35 42 1.9 1 0 42 36 47 1.9 1 0 47 37 37 1.9 1 0 37 38 35 1.9 1 0 35 39 40 1.9 1 0 40 40 41 1.9 1 0 41 41 48 1.9 1 0 48 42 55 1.9 1 0 55 43 49 1.9 1 0 49 44 35 1.9 1 0 35 45 44 1.9 1 0 44 46 43 1.9 1 0 43 47 47 1.9 1 0 47 48 44 1.9 1 0 44 49 46 1.9 1 0 46 50 34 1.9 1 0 34 51 40 1.9 1 0 40 52 58 1.9 1 1 57 53 27 1.9 1 0 27 54 39 1.9 1 0 39 55 37 1.9 1 0 37 56 48 1.9 1 0 48 57 42 1.9 1 0 42 58 36 1.9 1 0 36 59 42 1.9 1 0 42 60 59 1.9 1 1 58 61 45 1.9 1 0 45 62 35 1.9 1 0 35 63 31 1.9 1 0 31 64 32 1.9 1 0 32 65 25 1.9 1 0 25 66 23 1.9 1 0 23 67 35 1.9 1 0 35 68 28 1.9 1 1 27 69 47 1.9 1 0 47 70 27 1.9 1 0 27 71 29 1.9 1 0 29 72 28 1.9 1 0 28 73 22 1.9 1 0 22 74 30 1.9 1 0 30 75 21 1.9 1 0 21 76 20 1.9 1 0 20 77 33 1.9 1 0 33 78 23 1.9 1 0 23 79 35 1.9 1 0 35 80 29 1.9 1 0 29 81 29 1.9 1 0 29 82 32 1.9 1 0 32 83 31 1.9 1 0 31 84 32 1.9 1 0 32 85 27 1.9 1 0 27 86 24 1.9 1 0 24 87 24 1.9 1 0 24 88 29 1.9 1 0 29 89 21 1.9 1 0 21 90 27 1.9 1 0 27 91 25 1.9 1 1 24 92 23 1.9 1 0 23 93 22 1.9 1 0 22 94 22 1.9 1 0 22 95 12 1.9 1 0 12 96 10 1.9 1 0 10 97 15 1.9 1 0 15 98 23 1.9 1 0 23 99 13 1.9 1 0 13 100 3 1.9 1 0 3 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_5_s1_R1.fastq.gz ============================================= 31778715 sequences processed in total