SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_4_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_4_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 414.69 s (17 us/read; 3.52 M reads/minute). === Summary === Total reads processed: 24,341,968 Reads with adapters: 5,730,058 (23.5%) Reads written (passing filters): 24,341,968 (100.0%) Total basepairs processed: 2,138,379,836 bp Quality-trimmed: 7,229,586 bp (0.3%) Total written (filtered): 2,123,664,226 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5730058 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.1% C: 12.5% G: 34.6% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4437637 6085492.0 0 4437637 2 894680 1521373.0 0 894680 3 373576 380343.2 0 373576 4 11988 95085.8 0 11988 5 7986 23771.5 0 7986 6 2794 5942.9 0 2794 7 175 1485.7 0 175 8 175 371.4 0 175 9 222 92.9 0 33 189 10 243 23.2 1 4 239 11 65 5.8 1 1 64 12 8 1.5 1 0 8 13 5 1.5 1 0 5 14 3 1.5 1 0 3 15 2 1.5 1 0 2 16 6 1.5 1 0 6 17 8 1.5 1 0 8 18 8 1.5 1 0 8 19 13 1.5 1 0 13 20 8 1.5 1 0 8 21 3 1.5 1 0 3 22 2 1.5 1 0 2 23 9 1.5 1 0 9 24 6 1.5 1 0 6 25 7 1.5 1 0 7 26 12 1.5 1 0 12 27 23 1.5 1 1 22 28 11 1.5 1 0 11 29 11 1.5 1 0 11 30 2 1.5 1 0 2 31 2 1.5 1 0 2 32 11 1.5 1 0 11 33 2 1.5 1 0 2 34 7 1.5 1 0 7 35 7 1.5 1 0 7 36 4 1.5 1 0 4 37 4 1.5 1 0 4 38 4 1.5 1 0 4 39 5 1.5 1 0 5 40 4 1.5 1 0 4 41 3 1.5 1 0 3 42 5 1.5 1 0 5 43 3 1.5 1 0 3 44 6 1.5 1 0 6 45 10 1.5 1 0 10 46 13 1.5 1 0 13 47 18 1.5 1 0 18 48 4 1.5 1 0 4 49 6 1.5 1 0 6 50 13 1.5 1 0 13 51 12 1.5 1 0 12 52 9 1.5 1 0 9 53 14 1.5 1 0 14 54 1 1.5 1 0 1 55 11 1.5 1 0 11 56 4 1.5 1 0 4 57 6 1.5 1 0 6 58 2 1.5 1 0 2 59 5 1.5 1 0 5 60 2 1.5 1 0 2 61 4 1.5 1 0 4 62 4 1.5 1 0 4 63 6 1.5 1 0 6 64 4 1.5 1 0 4 65 4 1.5 1 0 4 66 2 1.5 1 0 2 67 7 1.5 1 1 6 68 1 1.5 1 0 1 69 7 1.5 1 0 7 70 4 1.5 1 0 4 71 6 1.5 1 0 6 72 2 1.5 1 0 2 73 12 1.5 1 0 12 74 2 1.5 1 0 2 75 6 1.5 1 0 6 76 11 1.5 1 0 11 77 2 1.5 1 0 2 78 6 1.5 1 0 6 79 3 1.5 1 0 3 80 7 1.5 1 0 7 81 6 1.5 1 0 6 82 7 1.5 1 0 7 83 6 1.5 1 0 6 84 5 1.5 1 0 5 85 5 1.5 1 0 5 86 6 1.5 1 0 6 87 4 1.5 1 0 4 88 5 1.5 1 0 5 89 4 1.5 1 0 4 90 7 1.5 1 0 7 91 1 1.5 1 0 1 92 2 1.5 1 0 2 93 1 1.5 1 0 1 94 3 1.5 1 0 3 95 3 1.5 1 0 3 96 3 1.5 1 0 3 97 3 1.5 1 0 3 98 2 1.5 1 0 2 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R2.fastq.gz ============================================= 24341968 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24341968 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 371452 (1.53%)