SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_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; user defined) 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 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 /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R1_001.fastq.gz 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 3034.05 s (32 us/read; 1.88 M reads/minute). === Summary === Total reads processed: 95,078,293 Reads with adapters: 58,848,167 (61.9%) Reads written (passing filters): 95,078,293 (100.0%) Total basepairs processed: 14,261,743,950 bp Quality-trimmed: 18,533,032 bp (0.1%) Total written (filtered): 12,932,762,956 bp (90.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58848167 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 15.8% G: 14.1% T: 30.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24724303 23769573.2 0 24724303 2 2192576 5942393.3 0 2192576 3 1042067 1485598.3 0 1042067 4 655261 371399.6 0 655261 5 477537 92849.9 0 477537 6 396153 23212.5 0 396153 7 423130 5803.1 0 423130 8 457423 1450.8 0 457423 9 424500 362.7 0 413006 11494 10 446196 90.7 1 415544 30652 11 465143 22.7 1 427929 37214 12 468903 5.7 1 434676 34227 13 448507 1.4 1 414045 34462 14 465166 1.4 1 427289 37877 15 459814 1.4 1 422900 36914 16 461078 1.4 1 422731 38347 17 475933 1.4 1 437158 38775 18 453848 1.4 1 419943 33905 19 447533 1.4 1 413539 33994 20 457023 1.4 1 421300 35723 21 463475 1.4 1 426882 36593 22 450325 1.4 1 416322 34003 23 463871 1.4 1 427287 36584 24 450594 1.4 1 411685 38909 25 449609 1.4 1 414677 34932 26 446248 1.4 1 411995 34253 27 452244 1.4 1 418059 34185 28 439004 1.4 1 407592 31412 29 440489 1.4 1 408593 31896 30 435869 1.4 1 407591 28278 31 427568 1.4 1 399209 28359 32 429685 1.4 1 401802 27883 33 423814 1.4 1 394888 28926 34 432669 1.4 1 403029 29640 35 425569 1.4 1 395136 30433 36 413069 1.4 1 386424 26645 37 417282 1.4 1 389564 27718 38 411299 1.4 1 384463 26836 39 422142 1.4 1 393672 28470 40 399257 1.4 1 373795 25462 41 393915 1.4 1 367460 26455 42 399370 1.4 1 372928 26442 43 407366 1.4 1 379096 28270 44 381801 1.4 1 352422 29379 45 534446 1.4 1 507061 27385 46 220922 1.4 1 202544 18378 47 368220 1.4 1 344111 24109 48 375094 1.4 1 350570 24524 49 364701 1.4 1 341114 23587 50 350179 1.4 1 326143 24036 51 366664 1.4 1 340938 25726 52 349018 1.4 1 326564 22454 53 334697 1.4 1 312062 22635 54 338534 1.4 1 315306 23228 55 336212 1.4 1 314235 21977 56 320047 1.4 1 298360 21687 57 321649 1.4 1 299684 21965 58 336816 1.4 1 315144 21672 59 289180 1.4 1 268762 20418 60 302150 1.4 1 282506 19644 61 289047 1.4 1 269271 19776 62 297706 1.4 1 277515 20191 63 286345 1.4 1 266938 19407 64 285442 1.4 1 266817 18625 65 248921 1.4 1 231411 17510 66 274014 1.4 1 254524 19490 67 298134 1.4 1 276712 21422 68 306160 1.4 1 284848 21312 69 288858 1.4 1 259564 29294 70 556317 1.4 1 531457 24860 71 55700 1.4 1 51368 4332 72 42209 1.4 1 36813 5396 73 118301 1.4 1 108470 9831 74 179033 1.4 1 166018 13015 75 191576 1.4 1 178006 13570 76 188227 1.4 1 174899 13328 77 182972 1.4 1 169832 13140 78 175656 1.4 1 162812 12844 79 169131 1.4 1 156733 12398 80 162761 1.4 1 151022 11739 81 156178 1.4 1 144598 11580 82 151404 1.4 1 140246 11158 83 144686 1.4 1 134062 10624 84 138872 1.4 1 128480 10392 85 132517 1.4 1 122836 9681 86 129438 1.4 1 119634 9804 87 125561 1.4 1 116434 9127 88 103118 1.4 1 94450 8668 89 97569 1.4 1 89261 8308 90 95148 1.4 1 87165 7983 91 91487 1.4 1 84101 7386 92 87383 1.4 1 80244 7139 93 81992 1.4 1 74884 7108 94 77741 1.4 1 71106 6635 95 72595 1.4 1 66315 6280 96 67892 1.4 1 61974 5918 97 62665 1.4 1 57134 5531 98 57692 1.4 1 52622 5070 99 53385 1.4 1 48487 4898 100 50323 1.4 1 45734 4589 101 46686 1.4 1 42289 4397 102 42837 1.4 1 38705 4132 103 39166 1.4 1 35204 3962 104 36994 1.4 1 33188 3806 105 34010 1.4 1 30482 3528 106 32507 1.4 1 29041 3466 107 29864 1.4 1 26595 3269 108 26390 1.4 1 23241 3149 109 23862 1.4 1 21026 2836 110 22353 1.4 1 19573 2780 111 19709 1.4 1 17428 2281 112 18468 1.4 1 16117 2351 113 17589 1.4 1 15276 2313 114 15699 1.4 1 13592 2107 115 15013 1.4 1 12954 2059 116 13696 1.4 1 11832 1864 117 13376 1.4 1 11519 1857 118 11439 1.4 1 9831 1608 119 10494 1.4 1 8923 1571 120 9208 1.4 1 7771 1437 121 8368 1.4 1 7017 1351 122 8186 1.4 1 6943 1243 123 9576 1.4 1 8158 1418 124 7534 1.4 1 6250 1284 125 7307 1.4 1 6055 1252 126 11486 1.4 1 10127 1359 127 10120 1.4 1 8809 1311 128 6795 1.4 1 5762 1033 129 6533 1.4 1 5639 894 130 8401 1.4 1 7399 1002 131 11952 1.4 1 10963 989 132 11110 1.4 1 10171 939 133 15296 1.4 1 14043 1253 134 13019 1.4 1 11987 1032 135 4296 1.4 1 3733 563 136 1761 1.4 1 1388 373 137 1288 1.4 1 1033 255 138 1262 1.4 1 1012 250 139 809 1.4 1 513 296 140 593 1.4 1 393 200 141 347 1.4 1 222 125 142 271 1.4 1 139 132 143 182 1.4 1 133 49 144 193 1.4 1 124 69 145 447 1.4 1 376 71 146 752 1.4 1 655 97 147 5650 1.4 1 5121 529 148 3130 1.4 1 2811 319 149 668 1.4 1 608 60 150 10162 1.4 1 9584 578 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R1_001.fastq.gz ============================================= 95078293 sequences processed in total