SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R2_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/Meth8_R2_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 2638.98 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 86,019,978 Reads with adapters: 57,885,033 (67.3%) Reads written (passing filters): 86,019,978 (100.0%) Total basepairs processed: 12,902,996,700 bp Quality-trimmed: 120,161,263 bp (0.9%) Total written (filtered): 11,046,493,995 bp (85.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57885033 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.1% C: 14.8% G: 20.5% T: 30.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16820582 21504994.5 0 16820582 2 1862286 5376248.6 0 1862286 3 936466 1344062.2 0 936466 4 605592 336015.5 0 605592 5 475487 84003.9 0 475487 6 398105 21001.0 0 398105 7 408347 5250.2 0 408347 8 471707 1312.6 0 471707 9 407942 328.1 0 401353 6589 10 439530 82.0 1 415296 24234 11 467816 20.5 1 432957 34859 12 520643 5.1 1 488863 31780 13 415938 1.3 1 383469 32469 14 466905 1.3 1 434195 32710 15 458557 1.3 1 427008 31549 16 492516 1.3 1 456792 35724 17 477379 1.3 1 445152 32227 18 451182 1.3 1 421421 29761 19 500424 1.3 1 468212 32212 20 494705 1.3 1 462934 31771 21 455003 1.3 1 422802 32201 22 486051 1.3 1 456395 29656 23 469019 1.3 1 439069 29950 24 503598 1.3 1 470321 33277 25 565563 1.3 1 533711 31852 26 409431 1.3 1 381032 28399 27 479240 1.3 1 447524 31716 28 466152 1.3 1 443935 22217 29 489845 1.3 1 463159 26686 30 479751 1.3 1 457328 22423 31 476875 1.3 1 453177 23698 32 478041 1.3 1 456431 21610 33 482644 1.3 1 458872 23772 34 507689 1.3 1 481041 26648 35 469306 1.3 1 444560 24746 36 496338 1.3 1 468972 27366 37 513606 1.3 1 488338 25268 38 451239 1.3 1 430247 20992 39 566543 1.3 1 542086 24457 40 405070 1.3 1 379663 25407 41 537051 1.3 1 504559 32492 42 499931 1.3 1 477755 22176 43 507165 1.3 1 466642 40523 44 1941183 1.3 1 1876477 64706 45 935552 1.3 1 897820 37732 46 501780 1.3 1 479910 21870 47 398760 1.3 1 384907 13853 48 175976 1.3 1 163182 12794 49 438207 1.3 1 420436 17771 50 323829 1.3 1 309651 14178 51 276691 1.3 1 262719 13972 52 411424 1.3 1 395723 15701 53 279200 1.3 1 264119 15081 54 563836 1.3 1 546949 16887 55 164834 1.3 1 153087 11747 56 444528 1.3 1 413264 31264 57 1514464 1.3 1 1474243 40221 58 279899 1.3 1 266737 13162 59 160998 1.3 1 145677 15321 60 809693 1.3 1 784650 25043 61 301140 1.3 1 286569 14571 62 445501 1.3 1 423540 21961 63 715056 1.3 1 689734 25322 64 656664 1.3 1 637998 18666 65 113751 1.3 1 107241 6510 66 146000 1.3 1 137093 8907 67 299921 1.3 1 289150 10771 68 208678 1.3 1 200605 8073 69 94632 1.3 1 88579 6053 70 187195 1.3 1 180159 7036 71 119160 1.3 1 113174 5986 72 141554 1.3 1 133747 7807 73 209527 1.3 1 199874 9653 74 230261 1.3 1 219752 10509 75 245790 1.3 1 234882 10908 76 197447 1.3 1 189638 7809 77 82092 1.3 1 77338 4754 78 119203 1.3 1 112733 6470 79 204760 1.3 1 195984 8776 80 243731 1.3 1 233374 10357 81 246576 1.3 1 236316 10260 82 240303 1.3 1 229689 10614 83 242699 1.3 1 232273 10426 84 232354 1.3 1 222463 9891 85 227598 1.3 1 217577 10021 86 209159 1.3 1 200090 9069 87 198649 1.3 1 190030 8619 88 191699 1.3 1 183327 8372 89 182515 1.3 1 174595 7920 90 178321 1.3 1 170410 7911 91 168801 1.3 1 161150 7651 92 158966 1.3 1 151850 7116 93 148659 1.3 1 141828 6831 94 138882 1.3 1 132247 6635 95 130280 1.3 1 123994 6286 96 124412 1.3 1 118631 5781 97 120129 1.3 1 114339 5790 98 113295 1.3 1 107862 5433 99 106685 1.3 1 101638 5047 100 99370 1.3 1 94497 4873 101 91066 1.3 1 86557 4509 102 82461 1.3 1 78359 4102 103 76536 1.3 1 72612 3924 104 69662 1.3 1 66047 3615 105 65495 1.3 1 61854 3641 106 61148 1.3 1 57699 3449 107 54909 1.3 1 51731 3178 108 49804 1.3 1 46602 3202 109 45055 1.3 1 42356 2699 110 40566 1.3 1 37953 2613 111 36910 1.3 1 34503 2407 112 33589 1.3 1 31217 2372 113 30757 1.3 1 28545 2212 114 27661 1.3 1 25585 2076 115 25344 1.3 1 23309 2035 116 23323 1.3 1 21399 1924 117 21198 1.3 1 19322 1876 118 18450 1.3 1 16795 1655 119 15973 1.3 1 14451 1522 120 14417 1.3 1 13027 1390 121 12683 1.3 1 11377 1306 122 11909 1.3 1 10563 1346 123 11431 1.3 1 10210 1221 124 9711 1.3 1 8589 1122 125 9421 1.3 1 8294 1127 126 12127 1.3 1 10879 1248 127 10697 1.3 1 9511 1186 128 7739 1.3 1 6747 992 129 7480 1.3 1 6576 904 130 10033 1.3 1 9013 1020 131 14306 1.3 1 13318 988 132 13444 1.3 1 12483 961 133 20433 1.3 1 19047 1386 134 15714 1.3 1 14483 1231 135 4673 1.3 1 4142 531 136 1959 1.3 1 1698 261 137 1427 1.3 1 1187 240 138 1111 1.3 1 894 217 139 717 1.3 1 579 138 140 701 1.3 1 507 194 141 455 1.3 1 310 145 142 292 1.3 1 214 78 143 267 1.3 1 195 72 144 243 1.3 1 175 68 145 514 1.3 1 451 63 146 575 1.3 1 514 61 147 3653 1.3 1 3383 270 148 1777 1.3 1 1589 188 149 436 1.3 1 389 47 150 5252 1.3 1 5061 191 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R2_001.fastq.gz ============================================= 86019978 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 86019978 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 845678 (0.98%)