SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/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 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_7_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 512.70 s (17 us/read; 3.46 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: /home/sam/Downloads/zr2096/Raw_data/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): 261111 (0.88%)