SUMMARISING RUN PARAMETERS ========================== Input filename: WGBS-Col-0-GSM1942127-SRR2922654_1.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4 Cutadapt version: 1.15 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 Output file will be GZIP compressed This is cutadapt 1.15 with Python 2.7.14+ Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC WGBS-Col-0-GSM1942127-SRR2922654_1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1346.72 s (46 us/read; 1.30 M reads/minute). === Summary === Total reads processed: 29,192,639 Reads with adapters: 7,235,606 (24.8%) Reads written (passing filters): 29,192,639 (100.0%) Total basepairs processed: 4,391,498,508 bp Quality-trimmed: 32,221,144 bp (0.7%) Total written (filtered): 4,350,054,310 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7235606 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.4% C: 3.0% G: 14.0% T: 39.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6061258 7298159.8 0 6061258 2 707257 1824539.9 0 707257 3 353510 456135.0 0 353510 4 103481 114033.7 0 103481 5 1143 28508.4 0 1143 6 1268 7127.1 0 1268 7 533 1781.8 0 533 8 193 445.4 0 193 9 336 111.4 0 97 239 10 812 27.8 1 94 718 11 551 7.0 1 39 512 12 345 1.7 1 63 282 13 127 0.4 1 1 126 14 200 0.4 1 24 176 15 100 0.4 1 10 90 16 126 0.4 1 14 112 17 177 0.4 1 55 122 18 243 0.4 1 72 171 19 111 0.4 1 15 96 20 25 0.4 1 6 19 21 106 0.4 1 30 76 22 106 0.4 1 20 86 23 105 0.4 1 23 82 24 142 0.4 1 21 121 25 76 0.4 1 22 54 26 78 0.4 1 8 70 27 23 0.4 1 3 20 28 18 0.4 1 4 14 29 61 0.4 1 15 46 30 89 0.4 1 17 72 31 95 0.4 1 5 90 32 45 0.4 1 7 38 33 65 0.4 1 6 59 34 26 0.4 1 3 23 35 49 0.4 1 3 46 36 24 0.4 1 5 19 37 52 0.4 1 5 47 38 76 0.4 1 8 68 39 93 0.4 1 11 82 40 28 0.4 1 3 25 41 45 0.4 1 5 40 42 57 0.4 1 8 49 43 25 0.4 1 6 19 44 40 0.4 1 2 38 45 26 0.4 1 5 21 46 57 0.4 1 5 52 47 76 0.4 1 10 66 48 49 0.4 1 2 47 49 71 0.4 1 14 57 50 79 0.4 1 10 69 51 27 0.4 1 2 25 52 33 0.4 1 5 28 53 58 0.4 1 8 50 54 56 0.4 1 5 51 55 13 0.4 1 0 13 56 27 0.4 1 3 24 57 69 0.4 1 4 65 58 16 0.4 1 1 15 59 26 0.4 1 0 26 60 54 0.4 1 9 45 61 12 0.4 1 1 11 62 22 0.4 1 3 19 63 31 0.4 1 5 26 64 46 0.4 1 9 37 65 42 0.4 1 5 37 66 48 0.4 1 5 43 67 31 0.4 1 4 27 68 42 0.4 1 2 40 69 49 0.4 1 3 46 70 55 0.4 1 5 50 71 51 0.4 1 3 48 72 48 0.4 1 4 44 73 48 0.4 1 4 44 74 23 0.4 1 2 21 75 25 0.4 1 2 23 76 31 0.4 1 4 27 77 26 0.4 1 1 25 78 32 0.4 1 2 30 79 40 0.4 1 8 32 80 32 0.4 1 1 31 81 34 0.4 1 3 31 82 40 0.4 1 2 38 83 39 0.4 1 5 34 84 44 0.4 1 2 42 85 21 0.4 1 1 20 86 36 0.4 1 5 31 87 25 0.4 1 1 24 88 29 0.4 1 1 28 89 40 0.4 1 1 39 90 37 0.4 1 2 35 91 19 0.4 1 2 17 92 34 0.4 1 5 29 93 24 0.4 1 3 21 94 20 0.4 1 0 20 95 23 0.4 1 1 22 96 21 0.4 1 3 18 97 14 0.4 1 0 14 98 16 0.4 1 0 16 99 20 0.4 1 1 19 100 20 0.4 1 0 20 101 17 0.4 1 0 17 102 13 0.4 1 0 13 103 15 0.4 1 3 12 104 23 0.4 1 4 19 105 20 0.4 1 1 19 106 16 0.4 1 3 13 107 19 0.4 1 2 17 108 9 0.4 1 1 8 109 6 0.4 1 1 5 110 9 0.4 1 1 8 111 8 0.4 1 0 8 112 13 0.4 1 0 13 113 8 0.4 1 0 8 114 3 0.4 1 1 2 115 6 0.4 1 1 5 116 6 0.4 1 0 6 117 7 0.4 1 2 5 118 5 0.4 1 1 4 119 5 0.4 1 0 5 120 6 0.4 1 0 6 121 5 0.4 1 0 5 122 2 0.4 1 0 2 123 3 0.4 1 0 3 124 3 0.4 1 0 3 125 4 0.4 1 0 4 126 3 0.4 1 0 3 127 3 0.4 1 1 2 128 4 0.4 1 0 4 129 3 0.4 1 0 3 130 4 0.4 1 0 4 131 2 0.4 1 1 1 132 1 0.4 1 0 1 134 2 0.4 1 0 2 135 1 0.4 1 0 1 138 1 0.4 1 0 1 140 1 0.4 1 0 1 141 2 0.4 1 0 2 151 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: WGBS-Col-0-GSM1942127-SRR2922654_1.fastq.gz ============================================= 29192639 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 585 (0.0%)