SUMMARISING RUN PARAMETERS ========================== Input filename: WGBS-Col-0-GSM2136441-SRR3465232_1.fastq.gz Trimming mode: paired-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 for both reads before a sequence pair 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-GSM2136441-SRR3465232_1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2606.41 s (35 us/read; 1.72 M reads/minute). === Summary === Total reads processed: 74,711,902 Reads with adapters: 12,903,776 (17.3%) Reads written (passing filters): 74,711,902 (100.0%) Total basepairs processed: 10,876,282,083 bp Quality-trimmed: 31,556,029 bp (0.3%) Total written (filtered): 10,823,793,324 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12903776 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 33.4% G: 20.4% T: 14.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9328070 18677975.5 0 9328070 2 2390403 4669493.9 0 2390403 3 977083 1167373.5 0 977083 4 90412 291843.4 0 90412 5 51321 72960.8 0 51321 6 10375 18240.2 0 10375 7 4900 4560.1 0 4900 8 474 1140.0 0 474 9 1639 285.0 0 265 1374 10 1485 71.3 1 223 1262 11 1526 17.8 1 119 1407 12 884 4.5 1 89 795 13 767 1.1 1 67 700 14 732 1.1 1 53 679 15 885 1.1 1 77 808 16 1087 1.1 1 125 962 17 1338 1.1 1 255 1083 18 1929 1.1 1 740 1189 19 1418 1.1 1 681 737 20 396 1.1 1 43 353 21 335 1.1 1 83 252 22 462 1.1 1 97 365 23 429 1.1 1 124 305 24 525 1.1 1 187 338 25 698 1.1 1 178 520 26 317 1.1 1 34 283 27 545 1.1 1 118 427 28 981 1.1 1 211 770 29 342 1.1 1 66 276 30 1785 1.1 1 78 1707 31 291 1.1 1 83 208 32 570 1.1 1 45 525 33 239 1.1 1 78 161 34 422 1.1 1 138 284 35 587 1.1 1 39 548 36 278 1.1 1 22 256 37 346 1.1 1 18 328 38 522 1.1 1 43 479 39 179 1.1 1 7 172 40 218 1.1 1 24 194 41 259 1.1 1 24 235 42 199 1.1 1 19 180 43 337 1.1 1 29 308 44 234 1.1 1 21 213 45 150 1.1 1 18 132 46 181 1.1 1 29 152 47 284 1.1 1 22 262 48 261 1.1 1 23 238 49 208 1.1 1 28 180 50 209 1.1 1 13 196 51 159 1.1 1 10 149 52 180 1.1 1 24 156 53 252 1.1 1 9 243 54 177 1.1 1 7 170 55 161 1.1 1 5 156 56 88 1.1 1 6 82 57 273 1.1 1 16 257 58 293 1.1 1 3 290 59 137 1.1 1 6 131 60 151 1.1 1 23 128 61 131 1.1 1 7 124 62 287 1.1 1 16 271 63 251 1.1 1 13 238 64 198 1.1 1 8 190 65 190 1.1 1 8 182 66 224 1.1 1 5 219 67 527 1.1 1 8 519 68 147 1.1 1 10 137 69 295 1.1 1 5 290 70 301 1.1 1 5 296 71 126 1.1 1 6 120 72 169 1.1 1 8 161 73 127 1.1 1 4 123 74 375 1.1 1 6 369 75 79 1.1 1 6 73 76 187 1.1 1 1 186 77 63 1.1 1 1 62 78 292 1.1 1 1 291 79 153 1.1 1 2 151 80 69 1.1 1 2 67 81 158 1.1 1 1 157 82 166 1.1 1 3 163 83 115 1.1 1 1 114 84 76 1.1 1 2 74 85 146 1.1 1 1 145 86 207 1.1 1 2 205 87 296 1.1 1 1 295 88 72 1.1 1 0 72 89 94 1.1 1 1 93 90 149 1.1 1 1 148 91 166 1.1 1 1 165 92 92 1.1 1 1 91 93 91 1.1 1 2 89 94 190 1.1 1 1 189 95 153 1.1 1 3 150 96 311 1.1 1 0 311 97 111 1.1 1 1 110 98 129 1.1 1 1 128 99 130 1.1 1 0 130 100 245 1.1 1 0 245 101 182 1.1 1 1 181 102 161 1.1 1 1 160 103 541 1.1 1 0 541 104 248 1.1 1 0 248 105 235 1.1 1 1 234 106 420 1.1 1 1 419 107 153 1.1 1 0 153 108 149 1.1 1 2 147 109 407 1.1 1 2 405 110 1474 1.1 1 2 1472 111 179 1.1 1 1 178 112 682 1.1 1 2 680 113 254 1.1 1 0 254 114 219 1.1 1 4 215 115 235 1.1 1 2 233 116 231 1.1 1 0 231 117 186 1.1 1 3 183 118 114 1.1 1 1 113 119 220 1.1 1 0 220 120 418 1.1 1 1 417 121 102 1.1 1 0 102 122 99 1.1 1 2 97 123 105 1.1 1 1 104 124 163 1.1 1 0 163 125 100 1.1 1 0 100 126 244 1.1 1 1 243 127 172 1.1 1 0 172 128 235 1.1 1 0 235 129 141 1.1 1 2 139 130 64 1.1 1 0 64 131 387 1.1 1 3 384 132 678 1.1 1 0 678 133 1030 1.1 1 0 1030 134 192 1.1 1 0 192 135 116 1.1 1 0 116 136 123 1.1 1 0 123 137 211 1.1 1 0 211 138 280 1.1 1 0 280 139 557 1.1 1 2 555 140 257 1.1 1 0 257 141 749 1.1 1 0 749 142 62 1.1 1 0 62 143 131 1.1 1 0 131 144 134 1.1 1 0 134 145 131 1.1 1 0 131 146 299 1.1 1 0 299 147 433 1.1 1 0 433 148 648 1.1 1 0 648 149 317 1.1 1 0 317 150 98 1.1 1 0 98 151 134 1.1 1 0 134 RUN STATISTICS FOR INPUT FILE: WGBS-Col-0-GSM2136441-SRR3465232_1.fastq.gz ============================================= 74711902 sequences processed in total