SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/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 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_1_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 511.08 s (18 us/read; 3.40 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: /home/sam/Downloads/zr2096/Raw_data/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): 379420 (1.31%)