SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.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 TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 553.52 s (19 us/read; 3.24 M reads/minute). === Summary === Total reads processed: 29,892,002 Reads with adapters: 13,088,943 (43.8%) Reads written (passing filters): 29,892,002 (100.0%) Total basepairs processed: 2,698,353,334 bp Quality-trimmed: 8,120,692 bp (0.3%) Total written (filtered): 2,674,123,947 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13088943 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.1% C: 6.8% G: 22.4% T: 43.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11066739 7473000.5 0 11066739 2 1369931 1868250.1 0 1369931 3 522764 467062.5 0 522764 4 82767 116765.6 0 82767 5 30112 29191.4 0 30112 6 8805 7297.9 0 8805 7 3969 1824.5 0 3969 8 96 456.1 0 96 9 69 114.0 0 12 57 10 158 28.5 1 1 157 11 106 7.1 1 0 106 12 56 1.8 1 0 56 13 57 1.8 1 0 57 14 100 1.8 1 0 100 15 40 1.8 1 0 40 16 41 1.8 1 0 41 17 37 1.8 1 0 37 18 60 1.8 1 0 60 19 44 1.8 1 0 44 20 47 1.8 1 0 47 21 45 1.8 1 1 44 22 45 1.8 1 0 45 23 64 1.8 1 2 62 24 38 1.8 1 0 38 25 53 1.8 1 0 53 26 68 1.8 1 0 68 27 45 1.8 1 0 45 28 60 1.8 1 0 60 29 46 1.8 1 0 46 30 71 1.8 1 0 71 31 41 1.8 1 0 41 32 47 1.8 1 0 47 33 50 1.8 1 0 50 34 40 1.8 1 0 40 35 49 1.8 1 0 49 36 37 1.8 1 0 37 37 35 1.8 1 0 35 38 43 1.8 1 0 43 39 52 1.8 1 0 52 40 43 1.8 1 0 43 41 58 1.8 1 0 58 42 55 1.8 1 0 55 43 40 1.8 1 0 40 44 36 1.8 1 0 36 45 33 1.8 1 0 33 46 48 1.8 1 0 48 47 37 1.8 1 0 37 48 42 1.8 1 0 42 49 42 1.8 1 0 42 50 40 1.8 1 0 40 51 37 1.8 1 1 36 52 46 1.8 1 0 46 53 37 1.8 1 0 37 54 45 1.8 1 0 45 55 43 1.8 1 1 42 56 38 1.8 1 0 38 57 38 1.8 1 0 38 58 41 1.8 1 0 41 59 36 1.8 1 0 36 60 44 1.8 1 1 43 61 32 1.8 1 0 32 62 33 1.8 1 0 33 63 31 1.8 1 0 31 64 52 1.8 1 0 52 65 27 1.8 1 0 27 66 37 1.8 1 0 37 67 31 1.8 1 0 31 68 24 1.8 1 0 24 69 45 1.8 1 0 45 70 33 1.8 1 0 33 71 36 1.8 1 0 36 72 34 1.8 1 0 34 73 32 1.8 1 0 32 74 39 1.8 1 0 39 75 32 1.8 1 0 32 76 20 1.8 1 0 20 77 34 1.8 1 0 34 78 34 1.8 1 0 34 79 31 1.8 1 0 31 80 27 1.8 1 0 27 81 22 1.8 1 0 22 82 25 1.8 1 0 25 83 42 1.8 1 0 42 84 32 1.8 1 0 32 85 24 1.8 1 0 24 86 32 1.8 1 1 31 87 44 1.8 1 0 44 88 32 1.8 1 0 32 89 16 1.8 1 0 16 90 25 1.8 1 0 25 91 32 1.8 1 0 32 92 22 1.8 1 0 22 93 28 1.8 1 0 28 94 22 1.8 1 0 22 95 7 1.8 1 0 7 96 24 1.8 1 0 24 97 16 1.8 1 0 16 98 20 1.8 1 1 19 99 7 1.8 1 0 7 100 1 1.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.fastq.gz ============================================= 29892002 sequences processed in total