SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_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/Meth16_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 2419.39 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 74,853,767 Reads with adapters: 46,193,449 (61.7%) Reads written (passing filters): 74,853,767 (100.0%) Total basepairs processed: 11,228,065,050 bp Quality-trimmed: 92,500,615 bp (0.8%) Total written (filtered): 9,861,964,532 bp (87.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46193449 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.2% C: 15.8% G: 18.5% T: 31.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16857444 18713441.8 0 16857444 2 1622265 4678360.4 0 1622265 3 776299 1169590.1 0 776299 4 493224 292397.5 0 493224 5 376158 73099.4 0 376158 6 296744 18274.8 0 296744 7 304967 4568.7 0 304967 8 369889 1142.2 0 369889 9 291515 285.5 0 286266 5249 10 331876 71.4 1 306820 25056 11 350023 17.8 1 317258 32765 12 383350 4.5 1 351569 31781 13 324899 1.1 1 293300 31599 14 353376 1.1 1 320030 33346 15 336985 1.1 1 307559 29426 16 368024 1.1 1 333022 35002 17 364381 1.1 1 331961 32420 18 323535 1.1 1 296706 26829 19 373153 1.1 1 342021 31132 20 362128 1.1 1 332288 29840 21 329167 1.1 1 299498 29669 22 361779 1.1 1 332770 29009 23 339307 1.1 1 312167 27140 24 357156 1.1 1 327333 29823 25 395068 1.1 1 365255 29813 26 306523 1.1 1 280923 25600 27 344334 1.1 1 316340 27994 28 332517 1.1 1 311683 20834 29 349643 1.1 1 326127 23516 30 343761 1.1 1 322652 21109 31 334410 1.1 1 313201 21209 32 333602 1.1 1 314043 19559 33 349550 1.1 1 327508 22042 34 347733 1.1 1 326392 21341 35 337882 1.1 1 313701 24181 36 341720 1.1 1 320203 21517 37 336767 1.1 1 315521 21246 38 345512 1.1 1 324065 21447 39 355935 1.1 1 335261 20674 40 289540 1.1 1 270519 19021 41 332171 1.1 1 313453 18718 42 340348 1.1 1 321277 19071 43 290012 1.1 1 272885 17127 44 360524 1.1 1 339659 20865 45 352868 1.1 1 332322 20546 46 290741 1.1 1 269895 20846 47 576533 1.1 1 551382 25151 48 185048 1.1 1 173744 11304 49 208224 1.1 1 194376 13848 50 307512 1.1 1 291995 15517 51 229463 1.1 1 214990 14473 52 282228 1.1 1 266076 16152 53 295164 1.1 1 277413 17751 54 409855 1.1 1 390576 19279 55 160564 1.1 1 148869 11695 56 301533 1.1 1 279491 22042 57 735948 1.1 1 704821 31127 58 151820 1.1 1 140872 10948 59 184867 1.1 1 170409 14458 60 523855 1.1 1 500022 23833 61 226970 1.1 1 214990 11980 62 165682 1.1 1 145373 20309 63 891407 1.1 1 856221 35186 64 292436 1.1 1 277290 15146 65 120691 1.1 1 113231 7460 66 120334 1.1 1 109477 10857 67 330872 1.1 1 316328 14544 68 157121 1.1 1 148039 9082 69 152687 1.1 1 143285 9402 70 186526 1.1 1 176575 9951 71 141762 1.1 1 134210 7552 72 95641 1.1 1 89155 6486 73 118673 1.1 1 111775 6898 74 103410 1.1 1 97126 6284 75 96060 1.1 1 89990 6070 76 86625 1.1 1 80634 5991 77 128061 1.1 1 120564 7497 78 149888 1.1 1 141351 8537 79 161524 1.1 1 152386 9138 80 168715 1.1 1 159693 9022 81 155231 1.1 1 146238 8993 82 152479 1.1 1 143566 8913 83 152323 1.1 1 143205 9118 84 146819 1.1 1 138296 8523 85 139114 1.1 1 130844 8270 86 128439 1.1 1 120886 7553 87 121266 1.1 1 114042 7224 88 115683 1.1 1 108677 7006 89 108535 1.1 1 101855 6680 90 106053 1.1 1 99659 6394 91 100638 1.1 1 94355 6283 92 95316 1.1 1 89239 6077 93 90370 1.1 1 84573 5797 94 89220 1.1 1 83422 5798 95 85775 1.1 1 80191 5584 96 81111 1.1 1 75808 5303 97 77518 1.1 1 72310 5208 98 72019 1.1 1 67119 4900 99 69206 1.1 1 64373 4833 100 65518 1.1 1 60840 4678 101 63416 1.1 1 58906 4510 102 55728 1.1 1 51605 4123 103 51631 1.1 1 47853 3778 104 53436 1.1 1 49417 4019 105 51115 1.1 1 47170 3945 106 52357 1.1 1 48203 4154 107 48910 1.1 1 44872 4038 108 41602 1.1 1 38286 3316 109 36896 1.1 1 33830 3066 110 35806 1.1 1 32728 3078 111 31185 1.1 1 28405 2780 112 29571 1.1 1 26831 2740 113 33046 1.1 1 29885 3161 114 32401 1.1 1 29445 2956 115 32639 1.1 1 29662 2977 116 39577 1.1 1 36305 3272 117 41766 1.1 1 38288 3478 118 33002 1.1 1 30170 2832 119 24880 1.1 1 22606 2274 120 22503 1.1 1 20446 2057 121 19739 1.1 1 17779 1960 122 19765 1.1 1 17879 1886 123 20347 1.1 1 18294 2053 124 17414 1.1 1 15558 1856 125 17667 1.1 1 15775 1892 126 32306 1.1 1 29360 2946 127 25114 1.1 1 22492 2622 128 15143 1.1 1 13567 1576 129 17373 1.1 1 15782 1591 130 48340 1.1 1 44582 3758 131 79909 1.1 1 74813 5096 132 71856 1.1 1 67349 4507 133 118930 1.1 1 111564 7366 134 98719 1.1 1 92294 6425 135 24161 1.1 1 22481 1680 136 7285 1.1 1 6641 644 137 5044 1.1 1 4491 553 138 3415 1.1 1 2921 494 139 1813 1.1 1 1542 271 140 1565 1.1 1 1302 263 141 768 1.1 1 620 148 142 524 1.1 1 369 155 143 442 1.1 1 324 118 144 848 1.1 1 726 122 145 2194 1.1 1 2052 142 146 2965 1.1 1 2682 283 147 20914 1.1 1 19232 1682 148 10587 1.1 1 9552 1035 149 2856 1.1 1 2604 252 150 34842 1.1 1 33103 1739 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R2_001.fastq.gz ============================================= 74853767 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 74853767 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1580710 (2.11%)