SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_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 /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 535.07 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 30,798,582 Reads with adapters: 7,597,858 (24.7%) Reads written (passing filters): 30,798,582 (100.0%) Total basepairs processed: 2,666,689,257 bp Quality-trimmed: 9,450,051 bp (0.4%) Total written (filtered): 2,647,320,826 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 7597858 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 21.7% C: 14.3% G: 35.6% T: 28.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5888183 7699645.5 0 5888183 2 1196023 1924911.4 0 1196023 3 476916 481227.8 0 476916 4 16920 120307.0 0 16920 5 12402 30076.7 0 12402 6 5297 7519.2 0 5297 7 477 1879.8 0 477 8 240 469.9 0 240 9 279 117.5 0 37 242 10 309 29.4 1 6 303 11 96 7.3 1 0 96 12 8 1.8 1 0 8 13 6 1.8 1 0 6 14 8 1.8 1 0 8 15 7 1.8 1 0 7 16 8 1.8 1 0 8 17 5 1.8 1 0 5 18 9 1.8 1 0 9 19 13 1.8 1 0 13 20 9 1.8 1 0 9 21 10 1.8 1 0 10 22 9 1.8 1 0 9 23 18 1.8 1 0 18 24 5 1.8 1 1 4 25 14 1.8 1 0 14 26 8 1.8 1 0 8 27 47 1.8 1 0 47 28 15 1.8 1 0 15 29 9 1.8 1 0 9 30 5 1.8 1 0 5 31 7 1.8 1 0 7 32 9 1.8 1 0 9 33 12 1.8 1 0 12 34 8 1.8 1 0 8 35 8 1.8 1 0 8 36 10 1.8 1 0 10 37 10 1.8 1 0 10 38 5 1.8 1 0 5 39 12 1.8 1 0 12 40 8 1.8 1 0 8 41 5 1.8 1 0 5 42 9 1.8 1 0 9 43 7 1.8 1 0 7 44 11 1.8 1 0 11 45 10 1.8 1 0 10 46 18 1.8 1 0 18 47 14 1.8 1 0 14 48 10 1.8 1 0 10 49 6 1.8 1 0 6 50 17 1.8 1 0 17 51 10 1.8 1 0 10 52 12 1.8 1 0 12 53 18 1.8 1 0 18 54 11 1.8 1 0 11 55 12 1.8 1 0 12 56 10 1.8 1 0 10 57 2 1.8 1 0 2 58 3 1.8 1 0 3 59 10 1.8 1 0 10 60 4 1.8 1 0 4 61 10 1.8 1 0 10 62 11 1.8 1 0 11 63 13 1.8 1 0 13 64 10 1.8 1 0 10 65 12 1.8 1 0 12 66 9 1.8 1 0 9 67 10 1.8 1 0 10 68 5 1.8 1 0 5 69 2 1.8 1 0 2 70 9 1.8 1 0 9 71 5 1.8 1 0 5 72 7 1.8 1 0 7 73 5 1.8 1 0 5 74 14 1.8 1 0 14 75 6 1.8 1 0 6 76 6 1.8 1 0 6 77 3 1.8 1 0 3 78 3 1.8 1 0 3 79 8 1.8 1 0 8 80 4 1.8 1 0 4 81 5 1.8 1 0 5 82 4 1.8 1 0 4 83 4 1.8 1 0 4 84 3 1.8 1 0 3 85 5 1.8 1 0 5 86 2 1.8 1 0 2 87 3 1.8 1 0 3 88 4 1.8 1 0 4 89 4 1.8 1 0 4 90 1 1.8 1 0 1 91 5 1.8 1 0 5 92 2 1.8 1 0 2 93 2 1.8 1 0 2 94 4 1.8 1 0 4 95 4 1.8 1 0 4 96 3 1.8 1 1 2 97 3 1.8 1 0 3 98 3 1.8 1 0 3 100 2 1.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R2.fastq.gz ============================================= 30798582 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 30798582 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 472976 (1.54%)