SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200306/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200306/Meth13_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2557.47 s (25 us/read; 2.37 M reads/minute). === Summary === Total reads processed: 100,994,125 Reads with adapters: 75,452,441 (74.7%) Reads written (passing filters): 100,994,125 (100.0%) Total basepairs processed: 15,133,841,085 bp Total written (filtered): 11,286,581,533 bp (74.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 75452441 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.8% C: 3.5% G: 42.0% T: 7.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16889854 25248531.2 0 16889854 2 1387092 6312132.8 0 1387092 3 993122 1578033.2 0 993122 4 431060 394508.3 0 431060 5 275682 98627.1 0 275682 6 233401 24656.8 0 233401 7 293154 6164.2 0 293154 8 291627 1541.0 0 291627 9 282078 385.3 0 278508 3570 10 329147 96.3 1 300652 28495 11 581523 24.1 1 522909 58614 12 349882 6.0 1 315325 34557 13 313904 1.5 1 280320 33584 14 311573 1.5 1 277270 34303 15 260519 1.5 1 232317 28202 16 280060 1.5 1 248629 31431 17 309633 1.5 1 275006 34627 18 299523 1.5 1 268511 31012 19 308381 1.5 1 275762 32619 20 319544 1.5 1 285436 34108 21 307838 1.5 1 274585 33253 22 346274 1.5 1 309836 36438 23 436976 1.5 1 390674 46302 24 385479 1.5 1 342645 42834 25 336519 1.5 1 300157 36362 26 286169 1.5 1 255735 30434 27 302039 1.5 1 269115 32924 28 505249 1.5 1 451790 53459 29 356797 1.5 1 316417 40380 30 333714 1.5 1 298431 35283 31 348698 1.5 1 311129 37569 32 367127 1.5 1 327760 39367 33 317415 1.5 1 282607 34808 34 352429 1.5 1 314640 37789 35 326336 1.5 1 290643 35693 36 339179 1.5 1 301577 37602 37 481410 1.5 1 429087 52323 38 448729 1.5 1 395717 53012 39 414453 1.5 1 370021 44432 40 544488 1.5 1 486617 57871 41 545768 1.5 1 486251 59517 42 474348 1.5 1 425187 49161 43 335612 1.5 1 295805 39807 44 363737 1.5 1 321199 42538 45 612969 1.5 1 550568 62401 46 236931 1.5 1 210315 26616 47 340836 1.5 1 303534 37302 48 428571 1.5 1 381101 47470 49 789485 1.5 1 705703 83782 50 421164 1.5 1 373382 47782 51 489216 1.5 1 432238 56978 52 533011 1.5 1 475013 57998 53 470642 1.5 1 418275 52367 54 823609 1.5 1 732350 91259 55 528241 1.5 1 470022 58219 56 413780 1.5 1 367680 46100 57 485033 1.5 1 430576 54457 58 739339 1.5 1 657723 81616 59 419372 1.5 1 371464 47908 60 857360 1.5 1 765572 91788 61 470376 1.5 1 417741 52635 62 433854 1.5 1 384546 49308 63 401851 1.5 1 356696 45155 64 433832 1.5 1 385879 47953 65 358350 1.5 1 317317 41033 66 444050 1.5 1 393209 50841 67 582832 1.5 1 515092 67740 68 746325 1.5 1 660769 85556 69 670332 1.5 1 580864 89468 70 2073202 1.5 1 1871175 202027 71 121451 1.5 1 105945 15506 72 52792 1.5 1 43475 9317 73 538152 1.5 1 472151 66001 74 1756813 1.5 1 1560951 195862 75 441617 1.5 1 389006 52611 76 504090 1.5 1 445913 58177 77 565547 1.5 1 500475 65072 78 426572 1.5 1 377709 48863 79 456994 1.5 1 404267 52727 80 462729 1.5 1 408983 53746 81 405931 1.5 1 358406 47525 82 437959 1.5 1 387478 50481 83 408216 1.5 1 360003 48213 84 562518 1.5 1 497661 64857 85 514509 1.5 1 454185 60324 86 424696 1.5 1 374471 50225 87 445051 1.5 1 391943 53108 88 443537 1.5 1 390586 52951 89 546419 1.5 1 481197 65222 90 499277 1.5 1 439779 59498 91 566915 1.5 1 498750 68165 92 375931 1.5 1 329894 46037 93 500854 1.5 1 440092 60762 94 547235 1.5 1 480575 66660 95 391331 1.5 1 343323 48008 96 422734 1.5 1 370502 52232 97 536091 1.5 1 469971 66120 98 532528 1.5 1 466445 66083 99 488932 1.5 1 428065 60867 100 500021 1.5 1 436747 63274 101 389481 1.5 1 340084 49397 102 384198 1.5 1 336082 48116 103 467887 1.5 1 408747 59140 104 410457 1.5 1 357935 52522 105 398892 1.5 1 347934 50958 106 628657 1.5 1 548475 80182 107 497594 1.5 1 432357 65237 108 499014 1.5 1 433694 65320 109 553229 1.5 1 481173 72056 110 382989 1.5 1 332050 50939 111 364439 1.5 1 316458 47981 112 405699 1.5 1 351377 54322 113 356009 1.5 1 308400 47609 114 619887 1.5 1 538428 81459 115 1146598 1.5 1 996001 150597 116 330227 1.5 1 283825 46402 117 447731 1.5 1 387042 60689 118 395667 1.5 1 341652 54015 119 446331 1.5 1 385057 61274 120 254368 1.5 1 218804 35564 121 257448 1.5 1 221667 35781 122 238783 1.5 1 205563 33220 123 250549 1.5 1 215898 34651 124 240416 1.5 1 206474 33942 125 321804 1.5 1 276819 44985 126 183366 1.5 1 157670 25696 127 148680 1.5 1 127230 21450 128 93397 1.5 1 80218 13179 129 76162 1.5 1 65344 10818 130 57264 1.5 1 49107 8157 131 74918 1.5 1 64528 10390 132 32450 1.5 1 27800 4650 133 11091 1.5 1 9620 1471 134 4995 1.5 1 4285 710 135 1217 1.5 1 1029 188 136 490 1.5 1 426 64 137 53 1.5 1 49 4 138 8 1.5 1 7 1 139 9 1.5 1 9 140 9 1.5 1 6 3 141 6 1.5 1 4 2 142 1 1.5 1 1 145 1 1.5 1 1 146 1 1.5 1 0 1 147 2 1.5 1 0 2 148 86 1.5 1 67 19 149 7 1.5 1 6 1 150 327 1.5 1 286 41 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R1_001.fastq.gz ============================================= 100994125 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5451098 (5.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 36165151 (35.8%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1139376) or CGA (49790870) in total: 50930246 (50.4%)