SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/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 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_3_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 519.95 s (17 us/read; 3.45 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: /home/sam/Downloads/zr2096/Raw_data/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): 343249 (1.15%)