SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_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_5_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 547.82 s (17 us/read; 3.48 M reads/minute). === Summary === Total reads processed: 31,778,715 Reads with adapters: 6,846,951 (21.5%) Reads written (passing filters): 31,778,715 (100.0%) Total basepairs processed: 2,877,311,782 bp Quality-trimmed: 9,863,732 bp (0.3%) Total written (filtered): 2,858,374,133 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6846951 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.3% C: 13.4% G: 33.2% T: 31.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5229812 7944678.8 0 5229812 2 1095891 1986169.7 0 1095891 3 489213 496542.4 0 489213 4 15569 124135.6 0 15569 5 10559 31033.9 0 10559 6 4110 7758.5 0 4110 7 221 1939.6 0 221 8 231 484.9 0 231 9 248 121.2 0 46 202 10 275 30.3 1 1 274 11 71 7.6 1 0 71 12 10 1.9 1 0 10 13 11 1.9 1 0 11 14 15 1.9 1 0 15 15 10 1.9 1 0 10 16 13 1.9 1 0 13 17 7 1.9 1 0 7 18 10 1.9 1 0 10 19 9 1.9 1 0 9 20 10 1.9 1 0 10 21 11 1.9 1 0 11 22 12 1.9 1 0 12 23 18 1.9 1 0 18 24 11 1.9 1 0 11 25 7 1.9 1 0 7 26 13 1.9 1 0 13 27 32 1.9 1 0 32 28 18 1.9 1 0 18 29 7 1.9 1 0 7 30 9 1.9 1 0 9 31 10 1.9 1 0 10 32 11 1.9 1 0 11 33 5 1.9 1 0 5 34 15 1.9 1 0 15 35 10 1.9 1 0 10 36 6 1.9 1 0 6 37 4 1.9 1 0 4 38 10 1.9 1 0 10 39 9 1.9 1 0 9 40 11 1.9 1 0 11 41 12 1.9 1 0 12 42 11 1.9 1 0 11 43 6 1.9 1 0 6 44 10 1.9 1 0 10 45 15 1.9 1 0 15 46 10 1.9 1 0 10 47 14 1.9 1 0 14 48 6 1.9 1 0 6 49 7 1.9 1 0 7 50 8 1.9 1 0 8 51 14 1.9 1 0 14 52 16 1.9 1 1 15 53 15 1.9 1 0 15 54 12 1.9 1 0 12 55 10 1.9 1 0 10 56 6 1.9 1 0 6 57 8 1.9 1 0 8 58 9 1.9 1 0 9 59 3 1.9 1 0 3 60 4 1.9 1 0 4 61 10 1.9 1 0 10 62 5 1.9 1 0 5 63 10 1.9 1 0 10 64 6 1.9 1 1 5 65 11 1.9 1 0 11 66 7 1.9 1 0 7 67 1 1.9 1 0 1 68 8 1.9 1 0 8 69 6 1.9 1 0 6 70 12 1.9 1 0 12 71 5 1.9 1 0 5 72 6 1.9 1 0 6 73 4 1.9 1 0 4 74 8 1.9 1 0 8 75 9 1.9 1 0 9 76 8 1.9 1 0 8 77 10 1.9 1 0 10 78 5 1.9 1 0 5 79 3 1.9 1 0 3 80 4 1.9 1 0 4 81 7 1.9 1 0 7 82 7 1.9 1 0 7 83 14 1.9 1 0 14 84 10 1.9 1 0 10 85 6 1.9 1 0 6 86 3 1.9 1 0 3 87 3 1.9 1 0 3 88 4 1.9 1 0 4 89 5 1.9 1 0 5 90 5 1.9 1 0 5 91 5 1.9 1 0 5 92 3 1.9 1 0 3 93 2 1.9 1 0 2 94 4 1.9 1 0 4 95 6 1.9 1 0 6 96 4 1.9 1 0 4 97 4 1.9 1 0 4 98 1 1.9 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R2.fastq.gz ============================================= 31778715 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 31778715 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 275434 (0.87%)