SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_3_s1_R2.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 GATCGTCGGACT /mnt/owl/nightingales/C_virginica/zr2096_3_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 515.82 s (17 us/read; 3.48 M reads/minute). === Summary === Total reads processed: 29,892,002 Reads with adapters: 6,569,375 (22.0%) Reads written (passing filters): 29,892,002 (100.0%) Total basepairs processed: 2,696,736,157 bp Quality-trimmed: 9,005,435 bp (0.3%) Total written (filtered): 2,678,973,518 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6569375 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.4% C: 15.5% G: 33.6% T: 28.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4997725 7473000.5 0 4997725 2 1065489 1868250.1 0 1065489 3 469883 467062.5 0 469883 4 16657 116765.6 0 16657 5 12123 29191.4 0 12123 6 5013 7297.9 0 5013 7 246 1824.5 0 246 8 256 456.1 0 256 9 348 114.0 0 46 302 10 509 28.5 1 4 505 11 134 7.1 1 0 134 12 13 1.8 1 0 13 13 10 1.8 1 0 10 14 13 1.8 1 0 13 15 5 1.8 1 1 4 16 8 1.8 1 0 8 17 9 1.8 1 0 9 18 13 1.8 1 0 13 19 21 1.8 1 0 21 20 9 1.8 1 0 9 21 11 1.8 1 0 11 22 17 1.8 1 0 17 23 17 1.8 1 0 17 24 10 1.8 1 0 10 25 8 1.8 1 0 8 26 17 1.8 1 0 17 27 66 1.8 1 0 66 28 16 1.8 1 0 16 29 8 1.8 1 0 8 30 12 1.8 1 0 12 31 7 1.8 1 0 7 32 16 1.8 1 0 16 33 12 1.8 1 0 12 34 12 1.8 1 0 12 35 13 1.8 1 0 13 36 18 1.8 1 0 18 37 9 1.8 1 0 9 38 12 1.8 1 0 12 39 18 1.8 1 0 18 40 9 1.8 1 0 9 41 8 1.8 1 0 8 42 16 1.8 1 0 16 43 14 1.8 1 0 14 44 13 1.8 1 0 13 45 16 1.8 1 0 16 46 23 1.8 1 0 23 47 18 1.8 1 0 18 48 24 1.8 1 0 24 49 12 1.8 1 0 12 50 15 1.8 1 0 15 51 10 1.8 1 0 10 52 15 1.8 1 0 15 53 10 1.8 1 0 10 54 10 1.8 1 0 10 55 7 1.8 1 0 7 56 12 1.8 1 0 12 57 3 1.8 1 0 3 58 14 1.8 1 0 14 59 5 1.8 1 0 5 60 13 1.8 1 0 13 61 10 1.8 1 0 10 62 13 1.8 1 0 13 63 19 1.8 1 0 19 64 15 1.8 1 0 15 65 10 1.8 1 0 10 66 19 1.8 1 0 19 67 13 1.8 1 0 13 68 8 1.8 1 0 8 69 11 1.8 1 0 11 70 8 1.8 1 0 8 71 13 1.8 1 0 13 72 13 1.8 1 0 13 73 11 1.8 1 0 11 74 13 1.8 1 0 13 75 7 1.8 1 0 7 76 18 1.8 1 0 18 77 4 1.8 1 0 4 78 5 1.8 1 0 5 79 11 1.8 1 0 11 80 9 1.8 1 0 9 81 5 1.8 1 0 5 82 6 1.8 1 0 6 83 9 1.8 1 0 9 84 9 1.8 1 0 9 85 6 1.8 1 0 6 86 3 1.8 1 0 3 87 1 1.8 1 0 1 88 2 1.8 1 0 2 89 6 1.8 1 0 6 90 2 1.8 1 0 2 91 11 1.8 1 0 11 92 6 1.8 1 0 6 93 5 1.8 1 0 5 94 6 1.8 1 0 6 95 5 1.8 1 0 5 96 7 1.8 1 0 7 97 2 1.8 1 0 2 98 1 1.8 1 0 1 99 3 1.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_3_s1_R2.fastq.gz ============================================= 29892002 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29892002 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 42085 (0.14%)