SUMMARISING RUN PARAMETERS ========================== Input filename: illumina_100K.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.4 Cutadapt version: 1.18 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 28700). Second best hit was smallRNA (count: 0) 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 Output file will be GZIP compressed This is cutadapt 1.18 with Python 3.5.1 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_100K.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 4.61 s (46 us/read; 1.30 M reads/minute). === Summary === Total reads processed: 100,000 Reads with adapters: 64,192 (64.2%) Reads written (passing filters): 100,000 (100.0%) Total basepairs processed: 15,000,000 bp Quality-trimmed: 124,497 bp (0.8%) Total written (filtered): 13,021,579 bp (86.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64192 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.0% C: 15.5% G: 11.6% T: 31.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 25485 25000.0 0 25485 2 2462 6250.0 0 2462 3 897 1562.5 0 897 4 634 390.6 0 634 5 453 97.7 0 453 6 478 24.4 0 478 7 495 6.1 0 495 8 383 1.5 0 383 9 453 0.4 0 442 11 10 476 0.1 1 440 36 11 382 0.0 1 351 31 12 440 0.0 1 409 31 13 372 0.0 1 336 36 14 460 0.0 1 430 30 15 484 0.0 1 447 37 16 375 0.0 1 345 30 17 407 0.0 1 374 33 18 464 0.0 1 430 34 19 463 0.0 1 431 32 20 397 0.0 1 359 38 21 455 0.0 1 421 34 22 388 0.0 1 356 32 23 444 0.0 1 403 41 24 376 0.0 1 347 29 25 402 0.0 1 368 34 26 484 0.0 1 445 39 27 389 0.0 1 355 34 28 370 0.0 1 336 34 29 382 0.0 1 344 38 30 429 0.0 1 392 37 31 418 0.0 1 387 31 32 370 0.0 1 339 31 33 313 0.0 1 288 25 34 398 0.0 1 370 28 35 379 0.0 1 348 31 36 377 0.0 1 350 27 37 402 0.0 1 380 22 38 383 0.0 1 347 36 39 349 0.0 1 324 25 40 365 0.0 1 342 23 41 296 0.0 1 276 20 42 351 0.0 1 317 34 43 348 0.0 1 327 21 44 314 0.0 1 286 28 45 363 0.0 1 336 27 46 288 0.0 1 267 21 47 312 0.0 1 287 25 48 397 0.0 1 359 38 49 307 0.0 1 280 27 50 330 0.0 1 301 29 51 378 0.0 1 354 24 52 307 0.0 1 294 13 53 293 0.0 1 269 24 54 250 0.0 1 238 12 55 304 0.0 1 280 24 56 311 0.0 1 282 29 57 287 0.0 1 263 24 58 287 0.0 1 262 25 59 276 0.0 1 246 30 60 262 0.0 1 248 14 61 286 0.0 1 268 18 62 283 0.0 1 262 21 63 350 0.0 1 326 24 64 177 0.0 1 161 16 65 268 0.0 1 255 13 66 261 0.0 1 241 20 67 233 0.0 1 219 14 68 276 0.0 1 249 27 69 276 0.0 1 259 17 70 202 0.0 1 188 14 71 239 0.0 1 223 16 72 230 0.0 1 216 14 73 267 0.0 1 246 21 74 268 0.0 1 242 26 75 204 0.0 1 187 17 76 217 0.0 1 200 17 77 243 0.0 1 229 14 78 258 0.0 1 235 23 79 279 0.0 1 247 32 80 286 0.0 1 255 31 81 331 0.0 1 316 15 82 452 0.0 1 416 36 83 597 0.0 1 540 57 84 806 0.0 1 742 64 85 745 0.0 1 680 65 86 483 0.0 1 459 24 87 331 0.0 1 314 17 88 285 0.0 1 266 19 89 238 0.0 1 226 12 90 172 0.0 1 153 19 91 158 0.0 1 150 8 92 141 0.0 1 125 16 93 132 0.0 1 117 15 94 116 0.0 1 106 10 95 120 0.0 1 110 10 96 138 0.0 1 124 14 97 114 0.0 1 105 9 98 124 0.0 1 118 6 99 112 0.0 1 103 9 100 107 0.0 1 97 10 101 121 0.0 1 112 9 102 102 0.0 1 91 11 103 105 0.0 1 95 10 104 108 0.0 1 101 7 105 105 0.0 1 97 8 106 117 0.0 1 98 19 107 105 0.0 1 96 9 108 90 0.0 1 76 14 109 103 0.0 1 90 13 110 77 0.0 1 68 9 111 87 0.0 1 80 7 112 90 0.0 1 79 11 113 84 0.0 1 75 9 114 83 0.0 1 73 10 115 98 0.0 1 86 12 116 85 0.0 1 76 9 117 91 0.0 1 81 10 118 91 0.0 1 81 10 119 74 0.0 1 64 10 120 58 0.0 1 52 6 121 73 0.0 1 61 12 122 67 0.0 1 59 8 123 66 0.0 1 59 7 124 57 0.0 1 52 5 125 77 0.0 1 73 4 126 61 0.0 1 54 7 127 56 0.0 1 49 7 128 56 0.0 1 50 6 129 37 0.0 1 33 4 130 54 0.0 1 50 4 131 51 0.0 1 43 8 132 27 0.0 1 23 4 133 28 0.0 1 25 3 134 26 0.0 1 21 5 135 24 0.0 1 22 2 136 27 0.0 1 25 2 137 12 0.0 1 11 1 138 20 0.0 1 17 3 139 17 0.0 1 14 3 140 17 0.0 1 17 141 21 0.0 1 15 6 142 20 0.0 1 16 4 143 5 0.0 1 3 2 144 5 0.0 1 2 3 145 6 0.0 1 3 3 146 3 0.0 1 1 2 147 1 0.0 1 0 1 149 4 0.0 1 2 2 150 1 0.0 1 0 1 RUN STATISTICS FOR INPUT FILE: illumina_100K.fastq.gz ============================================= 100000 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 637 (0.6%)