SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_7_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_7_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 549.70 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 29,534,746 Reads with adapters: 13,300,837 (45.0%) Reads written (passing filters): 29,534,746 (100.0%) Total basepairs processed: 2,711,811,528 bp Quality-trimmed: 8,678,708 bp (0.3%) Total written (filtered): 2,686,940,853 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13300837 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 28.0% C: 6.4% G: 21.3% T: 44.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11345362 7383686.5 0 11345362 2 1348726 1845921.6 0 1348726 3 476512 461480.4 0 476512 4 81590 115370.1 0 81590 5 31877 28842.5 0 31877 6 9281 7210.6 0 9281 7 4185 1802.7 0 4185 8 72 450.7 0 72 9 56 112.7 0 10 46 10 135 28.2 1 1 134 11 78 7.0 1 0 78 12 49 1.8 1 0 49 13 55 1.8 1 0 55 14 81 1.8 1 0 81 15 34 1.8 1 0 34 16 33 1.8 1 0 33 17 47 1.8 1 0 47 18 48 1.8 1 0 48 19 37 1.8 1 0 37 20 31 1.8 1 0 31 21 35 1.8 1 0 35 22 41 1.8 1 0 41 23 59 1.8 1 1 58 24 34 1.8 1 0 34 25 30 1.8 1 1 29 26 57 1.8 1 0 57 27 46 1.8 1 0 46 28 47 1.8 1 1 46 29 37 1.8 1 0 37 30 53 1.8 1 0 53 31 39 1.8 1 0 39 32 46 1.8 1 0 46 33 43 1.8 1 0 43 34 45 1.8 1 0 45 35 35 1.8 1 0 35 36 33 1.8 1 0 33 37 27 1.8 1 0 27 38 31 1.8 1 0 31 39 34 1.8 1 0 34 40 38 1.8 1 0 38 41 32 1.8 1 0 32 42 60 1.8 1 0 60 43 35 1.8 1 0 35 44 29 1.8 1 0 29 45 34 1.8 1 0 34 46 21 1.8 1 0 21 47 32 1.8 1 0 32 48 43 1.8 1 0 43 49 46 1.8 1 0 46 50 48 1.8 1 0 48 51 33 1.8 1 0 33 52 32 1.8 1 0 32 53 33 1.8 1 0 33 54 45 1.8 1 0 45 55 51 1.8 1 0 51 56 32 1.8 1 0 32 57 39 1.8 1 0 39 58 38 1.8 1 0 38 59 32 1.8 1 0 32 60 37 1.8 1 0 37 61 22 1.8 1 0 22 62 36 1.8 1 0 36 63 33 1.8 1 0 33 64 34 1.8 1 0 34 65 41 1.8 1 0 41 66 36 1.8 1 0 36 67 33 1.8 1 1 32 68 28 1.8 1 0 28 69 25 1.8 1 0 25 70 19 1.8 1 0 19 71 33 1.8 1 0 33 72 21 1.8 1 0 21 73 20 1.8 1 0 20 74 28 1.8 1 1 27 75 25 1.8 1 0 25 76 30 1.8 1 0 30 77 25 1.8 1 0 25 78 35 1.8 1 0 35 79 31 1.8 1 0 31 80 34 1.8 1 0 34 81 22 1.8 1 0 22 82 22 1.8 1 0 22 83 29 1.8 1 0 29 84 27 1.8 1 0 27 85 21 1.8 1 0 21 86 27 1.8 1 0 27 87 29 1.8 1 0 29 88 18 1.8 1 0 18 89 17 1.8 1 0 17 90 25 1.8 1 0 25 91 21 1.8 1 0 21 92 19 1.8 1 0 19 93 18 1.8 1 0 18 94 16 1.8 1 0 16 95 15 1.8 1 0 15 96 19 1.8 1 0 19 97 19 1.8 1 0 19 98 19 1.8 1 0 19 99 11 1.8 1 0 11 100 3 1.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R1.fastq.gz ============================================= 29534746 sequences processed in total