SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_1_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_1_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 512.43 s (18 us/read; 3.39 M reads/minute). === Summary === Total reads processed: 28,982,766 Reads with adapters: 6,081,102 (21.0%) Reads written (passing filters): 28,982,766 (100.0%) Total basepairs processed: 2,650,680,530 bp Quality-trimmed: 12,111,002 bp (0.5%) Total written (filtered): 2,630,377,175 bp (99.2%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6081102 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 20.0% C: 18.5% G: 33.6% T: 27.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4531715 7245691.5 0 4531715 2 1086759 1811422.9 0 1086759 3 419635 452855.7 0 419635 4 17753 113213.9 0 17753 5 14526 28303.5 0 14526 6 8480 7075.9 0 8480 7 575 1769.0 0 575 8 342 442.2 0 342 9 431 110.6 0 135 296 10 443 27.6 1 2 441 11 61 6.9 1 0 61 12 5 1.7 1 1 4 13 3 1.7 1 0 3 14 10 1.7 1 0 10 15 5 1.7 1 0 5 16 2 1.7 1 0 2 17 3 1.7 1 0 3 18 3 1.7 1 0 3 19 5 1.7 1 0 5 20 5 1.7 1 0 5 21 2 1.7 1 0 2 22 5 1.7 1 0 5 23 13 1.7 1 0 13 24 3 1.7 1 0 3 25 6 1.7 1 0 6 26 3 1.7 1 0 3 27 13 1.7 1 0 13 28 15 1.7 1 0 15 29 7 1.7 1 0 7 30 6 1.7 1 0 6 31 3 1.7 1 0 3 32 5 1.7 1 0 5 33 9 1.7 1 0 9 34 11 1.7 1 1 10 35 3 1.7 1 0 3 36 6 1.7 1 0 6 37 6 1.7 1 0 6 38 7 1.7 1 0 7 39 5 1.7 1 0 5 40 4 1.7 1 0 4 41 4 1.7 1 0 4 42 6 1.7 1 0 6 43 5 1.7 1 0 5 44 3 1.7 1 0 3 45 10 1.7 1 0 10 46 8 1.7 1 0 8 47 6 1.7 1 0 6 48 5 1.7 1 0 5 49 9 1.7 1 0 9 50 5 1.7 1 0 5 51 4 1.7 1 0 4 52 5 1.7 1 0 5 53 7 1.7 1 0 7 54 4 1.7 1 0 4 55 2 1.7 1 0 2 56 2 1.7 1 0 2 57 1 1.7 1 0 1 58 1 1.7 1 0 1 59 6 1.7 1 0 6 60 5 1.7 1 1 4 61 3 1.7 1 0 3 62 4 1.7 1 0 4 63 5 1.7 1 0 5 64 2 1.7 1 0 2 65 8 1.7 1 0 8 66 4 1.7 1 0 4 67 2 1.7 1 0 2 68 3 1.7 1 0 3 69 3 1.7 1 0 3 70 5 1.7 1 0 5 71 4 1.7 1 0 4 72 6 1.7 1 0 6 73 6 1.7 1 0 6 74 3 1.7 1 0 3 75 1 1.7 1 0 1 76 4 1.7 1 0 4 77 2 1.7 1 0 2 78 3 1.7 1 0 3 79 2 1.7 1 0 2 80 1 1.7 1 0 1 82 2 1.7 1 0 2 83 5 1.7 1 0 5 84 2 1.7 1 0 2 85 1 1.7 1 0 1 86 4 1.7 1 0 4 87 3 1.7 1 0 3 88 3 1.7 1 0 3 89 2 1.7 1 0 2 90 4 1.7 1 0 4 91 4 1.7 1 0 4 92 2 1.7 1 0 2 93 1 1.7 1 0 1 94 3 1.7 1 0 3 95 3 1.7 1 0 3 96 1 1.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_1_s1_R2.fastq.gz ============================================= 28982766 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 28982766 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 42647 (0.15%)