SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_7_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_7_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 518.93 s (18 us/read; 3.41 M reads/minute). === Summary === Total reads processed: 29,534,746 Reads with adapters: 5,991,787 (20.3%) Reads written (passing filters): 29,534,746 (100.0%) Total basepairs processed: 2,711,789,087 bp Quality-trimmed: 8,555,178 bp (0.3%) Total written (filtered): 2,695,158,789 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5991787 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.4% C: 13.8% G: 32.0% T: 30.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4490237 7383686.5 0 4490237 2 1005906 1845921.6 0 1005906 3 465034 461480.4 0 465034 4 14918 115370.1 0 14918 5 9836 28842.5 0 9836 6 4113 7210.6 0 4113 7 197 1802.7 0 197 8 200 450.7 0 200 9 237 112.7 0 29 208 10 321 28.2 1 7 314 11 78 7.0 1 0 78 12 8 1.8 1 0 8 13 4 1.8 1 0 4 14 8 1.8 1 0 8 15 6 1.8 1 0 6 16 8 1.8 1 0 8 17 5 1.8 1 0 5 18 13 1.8 1 0 13 19 19 1.8 1 0 19 20 7 1.8 1 0 7 21 7 1.8 1 0 7 22 9 1.8 1 0 9 23 8 1.8 1 0 8 24 5 1.8 1 0 5 25 9 1.8 1 0 9 26 13 1.8 1 0 13 27 23 1.8 1 0 23 28 26 1.8 1 0 26 29 11 1.8 1 0 11 30 9 1.8 1 0 9 31 8 1.8 1 0 8 32 9 1.8 1 0 9 33 11 1.8 1 0 11 34 15 1.8 1 0 15 35 2 1.8 1 0 2 36 15 1.8 1 0 15 37 2 1.8 1 0 2 38 13 1.8 1 0 13 39 10 1.8 1 0 10 40 12 1.8 1 0 12 41 2 1.8 1 0 2 42 4 1.8 1 0 4 43 10 1.8 1 0 10 44 12 1.8 1 0 12 45 10 1.8 1 0 10 46 3 1.8 1 0 3 47 15 1.8 1 0 15 48 12 1.8 1 0 12 49 9 1.8 1 0 9 50 17 1.8 1 0 17 51 14 1.8 1 0 14 52 6 1.8 1 0 6 53 9 1.8 1 0 9 54 10 1.8 1 0 10 55 10 1.8 1 0 10 56 11 1.8 1 0 11 57 8 1.8 1 0 8 58 5 1.8 1 0 5 59 5 1.8 1 0 5 60 6 1.8 1 0 6 61 7 1.8 1 0 7 62 9 1.8 1 0 9 63 11 1.8 1 0 11 64 8 1.8 1 0 8 65 5 1.8 1 0 5 66 4 1.8 1 0 4 67 8 1.8 1 0 8 68 6 1.8 1 0 6 69 6 1.8 1 0 6 70 10 1.8 1 0 10 71 7 1.8 1 0 7 72 9 1.8 1 0 9 73 6 1.8 1 0 6 74 5 1.8 1 0 5 75 6 1.8 1 0 6 76 7 1.8 1 0 7 77 10 1.8 1 0 10 78 9 1.8 1 0 9 79 7 1.8 1 0 7 80 1 1.8 1 0 1 81 10 1.8 1 0 10 82 5 1.8 1 0 5 83 10 1.8 1 0 10 84 7 1.8 1 0 7 85 3 1.8 1 0 3 86 5 1.8 1 0 5 87 5 1.8 1 0 5 88 5 1.8 1 0 5 89 5 1.8 1 0 5 90 3 1.8 1 0 3 91 4 1.8 1 0 4 92 4 1.8 1 0 4 93 4 1.8 1 0 4 94 10 1.8 1 0 10 95 4 1.8 1 0 4 96 6 1.8 1 0 6 97 3 1.8 1 0 3 98 2 1.8 1 0 2 99 1 1.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_7_s1_R2.fastq.gz ============================================= 29534746 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29534746 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 34224 (0.12%)