SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_8_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_8_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 517.69 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 29,761,837 Reads with adapters: 6,230,529 (20.9%) Reads written (passing filters): 29,761,837 (100.0%) Total basepairs processed: 2,705,142,381 bp Quality-trimmed: 9,093,824 bp (0.3%) Total written (filtered): 2,687,730,288 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6230529 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.5% C: 13.9% G: 32.7% T: 30.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4708845 7440459.2 0 4708845 2 1035200 1860114.8 0 1035200 3 454845 465028.7 0 454845 4 15837 116257.2 0 15837 5 10378 29064.3 0 10378 6 3993 7266.1 0 3993 7 162 1816.5 0 162 8 166 454.1 0 166 9 234 113.5 0 36 198 10 238 28.4 1 2 236 11 62 7.1 1 0 62 12 8 1.8 1 0 8 13 1 1.8 1 0 1 14 2 1.8 1 0 2 15 9 1.8 1 0 9 16 5 1.8 1 0 5 17 3 1.8 1 0 3 18 7 1.8 1 0 7 19 11 1.8 1 0 11 20 5 1.8 1 0 5 21 2 1.8 1 0 2 22 14 1.8 1 0 14 23 11 1.8 1 0 11 24 5 1.8 1 0 5 25 11 1.8 1 0 11 26 7 1.8 1 0 7 27 14 1.8 1 0 14 28 12 1.8 1 0 12 29 12 1.8 1 0 12 30 11 1.8 1 0 11 31 6 1.8 1 0 6 32 2 1.8 1 0 2 33 6 1.8 1 0 6 34 15 1.8 1 0 15 35 12 1.8 1 0 12 36 12 1.8 1 0 12 37 10 1.8 1 0 10 38 11 1.8 1 0 11 39 4 1.8 1 0 4 40 11 1.8 1 0 11 41 6 1.8 1 0 6 42 2 1.8 1 0 2 43 4 1.8 1 0 4 44 10 1.8 1 1 9 45 15 1.8 1 0 15 46 13 1.8 1 0 13 47 12 1.8 1 0 12 48 6 1.8 1 0 6 49 8 1.8 1 0 8 50 8 1.8 1 0 8 51 15 1.8 1 0 15 52 7 1.8 1 0 7 53 13 1.8 1 0 13 54 7 1.8 1 0 7 55 7 1.8 1 0 7 56 4 1.8 1 0 4 57 10 1.8 1 0 10 58 4 1.8 1 0 4 59 7 1.8 1 0 7 60 8 1.8 1 0 8 61 3 1.8 1 0 3 62 6 1.8 1 0 6 63 3 1.8 1 0 3 64 7 1.8 1 0 7 65 7 1.8 1 0 7 66 7 1.8 1 0 7 67 5 1.8 1 0 5 68 1 1.8 1 0 1 69 2 1.8 1 0 2 70 7 1.8 1 0 7 71 5 1.8 1 0 5 72 5 1.8 1 0 5 73 5 1.8 1 0 5 74 5 1.8 1 0 5 75 4 1.8 1 0 4 76 9 1.8 1 0 9 77 7 1.8 1 0 7 78 7 1.8 1 0 7 79 3 1.8 1 0 3 80 5 1.8 1 0 5 81 6 1.8 1 0 6 82 3 1.8 1 0 3 83 4 1.8 1 0 4 84 6 1.8 1 0 6 85 4 1.8 1 0 4 86 3 1.8 1 0 3 87 1 1.8 1 0 1 88 4 1.8 1 0 4 89 3 1.8 1 0 3 90 3 1.8 1 0 3 91 3 1.8 1 0 3 92 5 1.8 1 0 5 93 4 1.8 1 0 4 94 1 1.8 1 0 1 95 3 1.8 1 0 3 96 2 1.8 1 0 2 97 3 1.8 1 0 3 98 2 1.8 1 0 2 99 1 1.8 1 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R2.fastq.gz ============================================= 29761837 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29761837 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 278619 (0.94%)