SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_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_6_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 412.81 s (17 us/read; 3.52 M reads/minute). === Summary === Total reads processed: 24,237,290 Reads with adapters: 5,603,158 (23.1%) Reads written (passing filters): 24,237,290 (100.0%) Total basepairs processed: 2,140,665,258 bp Quality-trimmed: 7,420,892 bp (0.3%) Total written (filtered): 2,125,867,555 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5603158 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.3% C: 13.4% G: 34.3% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4305035 6059322.5 0 4305035 2 895820 1514830.6 0 895820 3 376833 378707.7 0 376833 4 12244 94676.9 0 12244 5 8415 23669.2 0 8415 6 3206 5917.3 0 3206 7 186 1479.3 0 186 8 162 369.8 0 162 9 239 92.5 0 31 208 10 291 23.1 1 9 282 11 84 5.8 1 1 83 12 5 1.4 1 0 5 13 6 1.4 1 0 6 14 5 1.4 1 0 5 15 7 1.4 1 0 7 16 7 1.4 1 0 7 17 8 1.4 1 0 8 18 10 1.4 1 0 10 19 12 1.4 1 0 12 20 2 1.4 1 0 2 21 6 1.4 1 0 6 22 14 1.4 1 0 14 23 17 1.4 1 0 17 24 8 1.4 1 0 8 25 6 1.4 1 0 6 26 10 1.4 1 0 10 27 25 1.4 1 0 25 28 8 1.4 1 0 8 29 8 1.4 1 0 8 30 10 1.4 1 0 10 31 11 1.4 1 0 11 32 8 1.4 1 0 8 33 5 1.4 1 0 5 34 7 1.4 1 0 7 35 13 1.4 1 0 13 36 16 1.4 1 0 16 37 9 1.4 1 0 9 38 10 1.4 1 0 10 39 13 1.4 1 0 13 40 6 1.4 1 0 6 41 8 1.4 1 1 7 42 7 1.4 1 0 7 43 6 1.4 1 0 6 44 7 1.4 1 0 7 45 15 1.4 1 0 15 46 18 1.4 1 0 18 47 9 1.4 1 0 9 48 7 1.4 1 0 7 49 8 1.4 1 0 8 50 11 1.4 1 0 11 51 13 1.4 1 0 13 52 11 1.4 1 0 11 53 16 1.4 1 0 16 54 10 1.4 1 0 10 55 7 1.4 1 0 7 56 7 1.4 1 0 7 57 6 1.4 1 0 6 58 7 1.4 1 0 7 59 5 1.4 1 0 5 60 6 1.4 1 0 6 61 5 1.4 1 0 5 62 5 1.4 1 0 5 63 19 1.4 1 0 19 64 14 1.4 1 0 14 65 7 1.4 1 0 7 66 7 1.4 1 0 7 67 1 1.4 1 0 1 68 3 1.4 1 0 3 69 5 1.4 1 0 5 70 9 1.4 1 0 9 71 4 1.4 1 0 4 72 5 1.4 1 0 5 73 8 1.4 1 0 8 74 6 1.4 1 0 6 75 5 1.4 1 0 5 76 2 1.4 1 0 2 77 2 1.4 1 0 2 78 7 1.4 1 0 7 79 4 1.4 1 0 4 80 6 1.4 1 0 6 81 3 1.4 1 0 3 82 2 1.4 1 0 2 83 3 1.4 1 0 3 84 3 1.4 1 0 3 85 7 1.4 1 0 7 86 4 1.4 1 0 4 87 3 1.4 1 0 3 88 4 1.4 1 0 4 89 4 1.4 1 0 4 90 2 1.4 1 0 2 91 3 1.4 1 0 3 92 3 1.4 1 0 3 93 3 1.4 1 0 3 94 2 1.4 1 0 2 95 8 1.4 1 0 8 96 4 1.4 1 0 4 97 1 1.4 1 0 1 98 2 1.4 1 0 2 99 1 1.4 1 0 1 100 1 1.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R2.fastq.gz ============================================= 24237290 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24237290 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 327797 (1.35%)