SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_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/Meth9_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 2604.91 s (30 us/read; 2.02 M reads/minute). === Summary === Total reads processed: 87,891,647 Reads with adapters: 61,760,471 (70.3%) Reads written (passing filters): 87,891,647 (100.0%) Total basepairs processed: 13,183,747,050 bp Quality-trimmed: 20,211,428 bp (0.2%) Total written (filtered): 11,221,722,276 bp (85.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 61760471 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 16.1% G: 17.1% T: 30.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16847785 21972911.8 0 16847785 2 1852562 5493227.9 0 1852562 3 940028 1373307.0 0 940028 4 636787 343326.7 0 636787 5 505072 85831.7 0 505072 6 434729 21457.9 0 434729 7 460541 5364.5 0 460541 8 507040 1341.1 0 507040 9 463907 335.3 0 452561 11346 10 490189 83.8 1 457837 32352 11 515269 21.0 1 476503 38766 12 523939 5.2 1 487963 35976 13 512531 1.3 1 475591 36940 14 524954 1.3 1 484361 40593 15 529048 1.3 1 489326 39722 16 528686 1.3 1 487936 40750 17 548705 1.3 1 505772 42933 18 525659 1.3 1 488883 36776 19 523246 1.3 1 484396 38850 20 536154 1.3 1 496531 39623 21 545243 1.3 1 504803 40440 22 534326 1.3 1 496047 38279 23 555291 1.3 1 514115 41176 24 544462 1.3 1 500084 44378 25 546278 1.3 1 507108 39170 26 542570 1.3 1 503738 38832 27 555912 1.3 1 516527 39385 28 541268 1.3 1 504927 36341 29 546883 1.3 1 510031 36852 30 543315 1.3 1 510810 32505 31 537576 1.3 1 503361 34215 32 543453 1.3 1 510494 32959 33 546960 1.3 1 511676 35284 34 547479 1.3 1 513822 33657 35 550355 1.3 1 513234 37121 36 547515 1.3 1 515057 32458 37 540863 1.3 1 506710 34153 38 545596 1.3 1 510749 34847 39 540110 1.3 1 507658 32452 40 543877 1.3 1 508430 35447 41 545948 1.3 1 511311 34637 42 538597 1.3 1 504629 33968 43 562723 1.3 1 525641 37082 44 527782 1.3 1 487958 39824 45 756131 1.3 1 720753 35378 46 293956 1.3 1 270790 23166 47 517489 1.3 1 485516 31973 48 555461 1.3 1 521925 33536 49 511675 1.3 1 480648 31027 50 495780 1.3 1 462655 33125 51 570245 1.3 1 534387 35858 52 482901 1.3 1 454046 28855 53 469185 1.3 1 440224 28961 54 507197 1.3 1 473672 33525 55 526725 1.3 1 495537 31188 56 468306 1.3 1 438797 29509 57 500587 1.3 1 470500 30087 58 489270 1.3 1 459200 30070 59 498438 1.3 1 468391 30047 60 437109 1.3 1 412409 24700 61 407719 1.3 1 381105 26614 62 482806 1.3 1 453063 29743 63 476252 1.3 1 448835 27417 64 403709 1.3 1 379697 24012 65 393985 1.3 1 366634 27351 66 486105 1.3 1 457155 28950 67 431735 1.3 1 403752 27983 68 472253 1.3 1 442031 30222 69 479947 1.3 1 437169 42778 70 905596 1.3 1 867697 37899 71 105233 1.3 1 98613 6620 72 64790 1.3 1 58098 6692 73 171445 1.3 1 157897 13548 74 293933 1.3 1 274796 19137 75 324541 1.3 1 303670 20871 76 322566 1.3 1 302046 20520 77 313353 1.3 1 293456 19897 78 301758 1.3 1 281871 19887 79 297598 1.3 1 278030 19568 80 287535 1.3 1 268721 18814 81 275059 1.3 1 256731 18328 82 267723 1.3 1 250149 17574 83 259659 1.3 1 242580 17079 84 248441 1.3 1 231791 16650 85 238711 1.3 1 222540 16171 86 234946 1.3 1 219137 15809 87 231444 1.3 1 216073 15371 88 192125 1.3 1 177715 14410 89 181724 1.3 1 167883 13841 90 179345 1.3 1 166288 13057 91 172807 1.3 1 160339 12468 92 164676 1.3 1 152659 12017 93 156315 1.3 1 144837 11478 94 148546 1.3 1 137273 11273 95 139633 1.3 1 129011 10622 96 131843 1.3 1 121808 10035 97 121878 1.3 1 112431 9447 98 113756 1.3 1 104673 9083 99 104871 1.3 1 96377 8494 100 98118 1.3 1 89912 8206 101 90616 1.3 1 83130 7486 102 83900 1.3 1 76596 7304 103 77645 1.3 1 70800 6845 104 72293 1.3 1 65576 6717 105 65800 1.3 1 59654 6146 106 60961 1.3 1 55290 5671 107 55557 1.3 1 50083 5474 108 50267 1.3 1 45252 5015 109 45409 1.3 1 40909 4500 110 41515 1.3 1 37237 4278 111 37359 1.3 1 33325 4034 112 34320 1.3 1 30438 3882 113 30858 1.3 1 27139 3719 114 27871 1.3 1 24445 3426 115 25839 1.3 1 22610 3229 116 23384 1.3 1 20352 3032 117 21732 1.3 1 18973 2759 118 19394 1.3 1 16726 2668 119 16607 1.3 1 14241 2366 120 14783 1.3 1 12829 1954 121 13033 1.3 1 11141 1892 122 12794 1.3 1 10895 1899 123 12514 1.3 1 10634 1880 124 11058 1.3 1 9266 1792 125 10738 1.3 1 9138 1600 126 13732 1.3 1 11811 1921 127 12336 1.3 1 10669 1667 128 8970 1.3 1 7699 1271 129 8909 1.3 1 7781 1128 130 10326 1.3 1 9071 1255 131 15906 1.3 1 14501 1405 132 15199 1.3 1 13819 1380 133 20022 1.3 1 18443 1579 134 18471 1.3 1 17024 1447 135 5387 1.3 1 4684 703 136 2162 1.3 1 1694 468 137 1478 1.3 1 1098 380 138 1120 1.3 1 826 294 139 703 1.3 1 461 242 140 647 1.3 1 427 220 141 424 1.3 1 241 183 142 283 1.3 1 156 127 143 189 1.3 1 128 61 144 187 1.3 1 114 73 145 307 1.3 1 229 78 146 767 1.3 1 633 134 147 5340 1.3 1 4694 646 148 3158 1.3 1 2707 451 149 736 1.3 1 638 98 150 11318 1.3 1 10443 875 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R1_001.fastq.gz ============================================= 87891647 sequences processed in total