SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_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/Meth2_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 2624.27 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 85,631,206 Reads with adapters: 57,282,255 (66.9%) Reads written (passing filters): 85,631,206 (100.0%) Total basepairs processed: 12,844,680,900 bp Quality-trimmed: 14,442,697 bp (0.1%) Total written (filtered): 11,233,059,088 bp (87.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57282255 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.0% C: 15.8% G: 14.4% T: 30.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19795384 21407801.5 0 19795384 2 1831157 5351950.4 0 1831157 3 926757 1337987.6 0 926757 4 603821 334496.9 0 603821 5 451652 83624.2 0 451652 6 378205 20906.1 0 378205 7 403795 5226.5 0 403795 8 436443 1306.6 0 436443 9 416103 326.7 0 406757 9346 10 426363 81.7 1 402339 24024 11 446359 20.4 1 416329 30030 12 454775 5.1 1 427595 27180 13 435206 1.3 1 407389 27817 14 449362 1.3 1 417876 31486 15 445789 1.3 1 416572 29217 16 454877 1.3 1 422647 32230 17 473255 1.3 1 440704 32551 18 443621 1.3 1 416449 27172 19 436922 1.3 1 408918 28004 20 450170 1.3 1 421296 28874 21 458905 1.3 1 428441 30464 22 447990 1.3 1 420221 27769 23 462431 1.3 1 432092 30339 24 454441 1.3 1 421550 32891 25 451733 1.3 1 423558 28175 26 448476 1.3 1 420062 28414 27 463444 1.3 1 434651 28793 28 444064 1.3 1 417304 26760 29 453434 1.3 1 425031 28403 30 447516 1.3 1 422943 24573 31 443184 1.3 1 417778 25406 32 445287 1.3 1 419896 25391 33 445565 1.3 1 419104 26461 34 449132 1.3 1 422627 26505 35 451421 1.3 1 425935 25486 36 440218 1.3 1 415669 24549 37 435745 1.3 1 409391 26354 38 450619 1.3 1 425510 25109 39 429021 1.3 1 403513 25508 40 442995 1.3 1 414651 28344 41 439170 1.3 1 413432 25738 42 438474 1.3 1 413080 25394 43 435312 1.3 1 406567 28745 44 421274 1.3 1 393142 28132 45 582594 1.3 1 557420 25174 46 255962 1.3 1 237698 18264 47 411180 1.3 1 387755 23425 48 415698 1.3 1 392491 23207 49 410487 1.3 1 387646 22841 50 401224 1.3 1 376899 24325 51 421955 1.3 1 395661 26294 52 400918 1.3 1 378962 21956 53 384978 1.3 1 362919 22059 54 393480 1.3 1 369548 23932 55 397328 1.3 1 375093 22235 56 378333 1.3 1 356612 21721 57 383643 1.3 1 361758 21885 58 404139 1.3 1 381578 22561 59 350550 1.3 1 329289 21261 60 363320 1.3 1 343784 19536 61 350627 1.3 1 329853 20774 62 362636 1.3 1 341936 20700 63 360017 1.3 1 339842 20175 64 356810 1.3 1 337476 19334 65 309023 1.3 1 289593 19430 66 349962 1.3 1 329415 20547 67 384101 1.3 1 361320 22781 68 402653 1.3 1 379441 23212 69 386721 1.3 1 353320 33401 70 775481 1.3 1 747274 28207 71 54931 1.3 1 50767 4164 72 36204 1.3 1 30507 5697 73 145730 1.3 1 135258 10472 74 237568 1.3 1 223313 14255 75 262450 1.3 1 246765 15685 76 261106 1.3 1 245979 15127 77 253230 1.3 1 238354 14876 78 246727 1.3 1 232073 14654 79 241945 1.3 1 227824 14121 80 234723 1.3 1 220518 14205 81 226410 1.3 1 212580 13830 82 220415 1.3 1 206778 13637 83 212539 1.3 1 199447 13092 84 205272 1.3 1 192875 12397 85 199845 1.3 1 187200 12645 86 191977 1.3 1 179982 11995 87 186256 1.3 1 175066 11190 88 168380 1.3 1 157286 11094 89 160652 1.3 1 150136 10516 90 153355 1.3 1 143204 10151 91 147798 1.3 1 137811 9987 92 140599 1.3 1 131205 9394 93 133705 1.3 1 124506 9199 94 127557 1.3 1 118673 8884 95 119487 1.3 1 111135 8352 96 113036 1.3 1 104884 8152 97 105294 1.3 1 97714 7580 98 97352 1.3 1 90031 7321 99 90866 1.3 1 84090 6776 100 85764 1.3 1 79214 6550 101 78122 1.3 1 72042 6080 102 73307 1.3 1 67567 5740 103 66894 1.3 1 61496 5398 104 62019 1.3 1 56826 5193 105 57172 1.3 1 52392 4780 106 53365 1.3 1 48680 4685 107 47995 1.3 1 43740 4255 108 43150 1.3 1 39165 3985 109 38484 1.3 1 34589 3895 110 34526 1.3 1 31071 3455 111 30197 1.3 1 27169 3028 112 27267 1.3 1 24402 2865 113 23584 1.3 1 20947 2637 114 21658 1.3 1 19157 2501 115 19636 1.3 1 17249 2387 116 16977 1.3 1 15025 1952 117 16062 1.3 1 14069 1993 118 13357 1.3 1 11596 1761 119 11489 1.3 1 9980 1509 120 9838 1.3 1 8454 1384 121 8673 1.3 1 7392 1281 122 8237 1.3 1 6894 1343 123 7662 1.3 1 6581 1081 124 6589 1.3 1 5524 1065 125 6886 1.3 1 5892 994 126 13226 1.3 1 11580 1646 127 12563 1.3 1 10921 1642 128 6272 1.3 1 5312 960 129 4969 1.3 1 4215 754 130 7569 1.3 1 6615 954 131 13966 1.3 1 12777 1189 132 17450 1.3 1 16079 1371 133 26703 1.3 1 24688 2015 134 28492 1.3 1 26527 1965 135 8982 1.3 1 8237 745 136 2813 1.3 1 2354 459 137 1891 1.3 1 1505 386 138 1471 1.3 1 1145 326 139 676 1.3 1 490 186 140 603 1.3 1 430 173 141 222 1.3 1 134 88 142 166 1.3 1 109 57 143 147 1.3 1 104 43 144 316 1.3 1 241 75 145 1193 1.3 1 988 205 146 1174 1.3 1 937 237 147 6957 1.3 1 5785 1172 148 4324 1.3 1 3523 801 149 1611 1.3 1 1370 241 150 20493 1.3 1 17957 2536 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R1_001.fastq.gz ============================================= 85631206 sequences processed in total