SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_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/Meth17_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 2572.46 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 84,066,692 Reads with adapters: 51,628,964 (61.4%) Reads written (passing filters): 84,066,692 (100.0%) Total basepairs processed: 12,610,003,800 bp Quality-trimmed: 119,212,960 bp (0.9%) Total written (filtered): 10,895,096,635 bp (86.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 51628964 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.4% C: 16.5% G: 19.6% T: 30.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17596614 21016673.0 0 17596614 2 1876603 5254168.2 0 1876603 3 848089 1313542.1 0 848089 4 522037 328385.5 0 522037 5 390819 82096.4 0 390819 6 312330 20524.1 0 312330 7 323086 5131.0 0 323086 8 384719 1282.8 0 384719 9 304627 320.7 0 299432 5195 10 346691 80.2 1 322847 23844 11 370811 20.0 1 339969 30842 12 398407 5.0 1 368415 29992 13 336693 1.3 1 306493 30200 14 362589 1.3 1 331980 30609 15 357043 1.3 1 328991 28052 16 384496 1.3 1 352384 32112 17 377909 1.3 1 348350 29559 18 340317 1.3 1 314345 25972 19 385242 1.3 1 356518 28724 20 381087 1.3 1 352543 28544 21 346065 1.3 1 317243 28822 22 374572 1.3 1 347570 27002 23 358215 1.3 1 332551 25664 24 385711 1.3 1 356265 29446 25 445897 1.3 1 416193 29704 26 315169 1.3 1 290542 24627 27 347318 1.3 1 321297 26021 28 364911 1.3 1 343974 20937 29 372169 1.3 1 348834 23335 30 373789 1.3 1 352206 21583 31 355313 1.3 1 334448 20865 32 362329 1.3 1 342152 20177 33 362347 1.3 1 340897 21450 34 365197 1.3 1 344929 20268 35 365653 1.3 1 343806 21847 36 404456 1.3 1 380334 24122 37 421614 1.3 1 398328 23286 38 328632 1.3 1 308282 20350 39 368820 1.3 1 348244 20576 40 345256 1.3 1 326285 18971 41 333822 1.3 1 314094 19728 42 375664 1.3 1 357113 18551 43 325895 1.3 1 306952 18943 44 397677 1.3 1 376990 20687 45 412905 1.3 1 389790 23115 46 323571 1.3 1 301249 22322 47 662220 1.3 1 635126 27094 48 186131 1.3 1 175107 11024 49 242071 1.3 1 226983 15088 50 337981 1.3 1 322379 15602 51 254512 1.3 1 239559 14953 52 317286 1.3 1 300612 16674 53 334133 1.3 1 315176 18957 54 481387 1.3 1 460504 20883 55 171783 1.3 1 159671 12112 56 351691 1.3 1 325142 26549 57 1049962 1.3 1 1009065 40897 58 162928 1.3 1 151562 11366 59 191403 1.3 1 175847 15556 60 657588 1.3 1 629906 27682 61 240014 1.3 1 227808 12206 62 180294 1.3 1 158394 21900 63 1090354 1.3 1 1049491 40863 64 371407 1.3 1 353763 17644 65 121749 1.3 1 114357 7392 66 137669 1.3 1 126158 11511 67 386046 1.3 1 370046 16000 68 169521 1.3 1 159924 9597 69 175643 1.3 1 165266 10377 70 229207 1.3 1 218045 11162 71 153671 1.3 1 145986 7685 72 105674 1.3 1 99091 6583 73 135749 1.3 1 128411 7338 74 119862 1.3 1 113003 6859 75 113631 1.3 1 106722 6909 76 102562 1.3 1 95696 6866 77 158583 1.3 1 149993 8590 78 195568 1.3 1 185175 10393 79 210630 1.3 1 199653 10977 80 217624 1.3 1 206053 11571 81 202701 1.3 1 191804 10897 82 198674 1.3 1 187247 11427 83 198721 1.3 1 187336 11385 84 194231 1.3 1 183303 10928 85 185583 1.3 1 174855 10728 86 172860 1.3 1 162855 10005 87 166823 1.3 1 157228 9595 88 159356 1.3 1 150511 8845 89 151109 1.3 1 142788 8321 90 147078 1.3 1 138515 8563 91 141921 1.3 1 133402 8519 92 133838 1.3 1 125675 8163 93 127909 1.3 1 120415 7494 94 126574 1.3 1 118664 7910 95 121930 1.3 1 114589 7341 96 114793 1.3 1 107748 7045 97 111404 1.3 1 104365 7039 98 102307 1.3 1 95914 6393 99 98993 1.3 1 92344 6649 100 95094 1.3 1 88961 6133 101 92056 1.3 1 85876 6180 102 81668 1.3 1 76175 5493 103 77292 1.3 1 72021 5271 104 80472 1.3 1 74852 5620 105 77771 1.3 1 72360 5411 106 78781 1.3 1 72914 5867 107 72848 1.3 1 67770 5078 108 62794 1.3 1 58284 4510 109 54674 1.3 1 50325 4349 110 52500 1.3 1 48537 3963 111 47592 1.3 1 43699 3893 112 43337 1.3 1 39662 3675 113 47630 1.3 1 43516 4114 114 45743 1.3 1 41822 3921 115 44781 1.3 1 40993 3788 116 52207 1.3 1 48070 4137 117 57587 1.3 1 53150 4437 118 45114 1.3 1 41658 3456 119 37140 1.3 1 34085 3055 120 32976 1.3 1 30215 2761 121 28006 1.3 1 25649 2357 122 31197 1.3 1 28425 2772 123 30475 1.3 1 27646 2829 124 26611 1.3 1 24233 2378 125 26522 1.3 1 24060 2462 126 52087 1.3 1 47255 4832 127 40055 1.3 1 35874 4181 128 22200 1.3 1 20009 2191 129 26333 1.3 1 24293 2040 130 78462 1.3 1 73222 5240 131 135081 1.3 1 127507 7574 132 132315 1.3 1 124593 7722 133 246060 1.3 1 231560 14500 134 222036 1.3 1 208328 13708 135 53528 1.3 1 49894 3634 136 14149 1.3 1 12838 1311 137 9467 1.3 1 8436 1031 138 5758 1.3 1 4958 800 139 3211 1.3 1 2701 510 140 2670 1.3 1 2284 386 141 1106 1.3 1 931 175 142 724 1.3 1 614 110 143 728 1.3 1 585 143 144 1567 1.3 1 1317 250 145 5038 1.3 1 4675 363 146 5433 1.3 1 4752 681 147 37204 1.3 1 33274 3930 148 19138 1.3 1 16850 2288 149 6176 1.3 1 5472 704 150 79055 1.3 1 74226 4829 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R2_001.fastq.gz ============================================= 84066692 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 84066692 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2457196 (2.92%)