SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_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; auto-detected) 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/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 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth15_R1_001.fastq.gz_qual_trimmed.fastq 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 2660.07 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 109,570,006 Reads with adapters: 85,450,494 (78.0%) Reads written (passing filters): 109,570,006 (100.0%) Total basepairs processed: 16,418,442,294 bp Total written (filtered): 11,708,570,940 bp (71.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 85450494 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.5% C: 3.1% G: 43.1% T: 6.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15881685 27392501.5 0 15881685 2 1326314 6848125.4 0 1326314 3 987908 1712031.3 0 987908 4 479892 428007.8 0 479892 5 315963 107002.0 0 315963 6 284231 26750.5 0 284231 7 332502 6687.6 0 332502 8 336661 1671.9 0 336661 9 319375 418.0 0 315014 4361 10 376078 104.5 1 343524 32554 11 652211 26.1 1 584608 67603 12 385526 6.5 1 346589 38937 13 367125 1.6 1 327068 40057 14 345421 1.6 1 306617 38804 15 308922 1.6 1 274813 34109 16 325782 1.6 1 288166 37616 17 343774 1.6 1 304581 39193 18 351421 1.6 1 313771 37650 19 366477 1.6 1 326737 39740 20 357719 1.6 1 318838 38881 21 355737 1.6 1 316455 39282 22 396415 1.6 1 353903 42512 23 534508 1.6 1 476805 57703 24 438039 1.6 1 388134 49905 25 392153 1.6 1 349639 42514 26 326147 1.6 1 290198 35949 27 367964 1.6 1 326870 41094 28 589600 1.6 1 526234 63366 29 392793 1.6 1 347702 45091 30 371448 1.6 1 331148 40300 31 385679 1.6 1 343409 42270 32 413960 1.6 1 368784 45176 33 380206 1.6 1 337064 43142 34 433647 1.6 1 385023 48624 35 384518 1.6 1 341965 42553 36 393763 1.6 1 350251 43512 37 524656 1.6 1 465666 58990 38 548952 1.6 1 487732 61220 39 538971 1.6 1 481224 57747 40 575079 1.6 1 510147 64932 41 629906 1.6 1 558113 71793 42 406006 1.6 1 361276 44730 43 509761 1.6 1 450931 58830 44 418557 1.6 1 367831 50726 45 657598 1.6 1 588206 69392 46 301467 1.6 1 266028 35439 47 384563 1.6 1 341752 42811 48 479560 1.6 1 424891 54669 49 919153 1.6 1 819152 100001 50 482536 1.6 1 425678 56858 51 565122 1.6 1 496604 68518 52 646514 1.6 1 574128 72386 53 520868 1.6 1 461228 59640 54 954083 1.6 1 846167 107916 55 621495 1.6 1 550973 70522 56 475172 1.6 1 421258 53914 57 568249 1.6 1 502917 65332 58 866998 1.6 1 768288 98710 59 472499 1.6 1 416890 55609 60 1000128 1.6 1 890090 110038 61 558077 1.6 1 493433 64644 62 505737 1.6 1 447064 58673 63 455947 1.6 1 403334 52613 64 520537 1.6 1 461227 59310 65 422608 1.6 1 372821 49787 66 506601 1.6 1 446321 60280 67 681931 1.6 1 600525 81406 68 844668 1.6 1 744047 100621 69 797831 1.6 1 685016 112815 70 2455220 1.6 1 2209337 245883 71 165028 1.6 1 143638 21390 72 75859 1.6 1 63042 12817 73 627173 1.6 1 547548 79625 74 2053322 1.6 1 1816689 236633 75 504092 1.6 1 440997 63095 76 600709 1.6 1 529073 71636 77 637126 1.6 1 560130 76996 78 494842 1.6 1 435516 59326 79 522272 1.6 1 459493 62779 80 543212 1.6 1 477983 65229 81 465519 1.6 1 409098 56421 82 504755 1.6 1 443375 61380 83 475264 1.6 1 417280 57984 84 699035 1.6 1 614950 84085 85 611586 1.6 1 536803 74783 86 490097 1.6 1 429187 60910 87 577172 1.6 1 506192 70980 88 521333 1.6 1 456853 64480 89 634181 1.6 1 555529 78652 90 593188 1.6 1 519930 73258 91 679111 1.6 1 594973 84138 92 471265 1.6 1 412028 59237 93 583880 1.6 1 510091 73789 94 660442 1.6 1 577533 82909 95 454088 1.6 1 395746 58342 96 489013 1.6 1 425639 63374 97 636451 1.6 1 554620 81831 98 619482 1.6 1 539222 80260 99 550951 1.6 1 478829 72122 100 611930 1.6 1 531343 80587 101 477720 1.6 1 414868 62852 102 469210 1.6 1 406380 62830 103 559469 1.6 1 485715 73754 104 496435 1.6 1 429327 67108 105 478535 1.6 1 413559 64976 106 774275 1.6 1 669839 104436 107 617133 1.6 1 532627 84506 108 613075 1.6 1 527738 85337 109 696205 1.6 1 600909 95296 110 467767 1.6 1 403306 64461 111 444303 1.6 1 381719 62584 112 518609 1.6 1 446790 71819 113 446848 1.6 1 383017 63831 114 756680 1.6 1 650302 106378 115 1428651 1.6 1 1230013 198638 116 451175 1.6 1 384952 66223 117 589655 1.6 1 504024 85631 118 583890 1.6 1 498851 85039 119 633978 1.6 1 541847 92131 120 357006 1.6 1 304026 52980 121 371769 1.6 1 316182 55587 122 339599 1.6 1 289245 50354 123 378713 1.6 1 322408 56305 124 381818 1.6 1 324294 57524 125 491769 1.6 1 417384 74385 126 304155 1.6 1 257227 46928 127 265411 1.6 1 224767 40644 128 173625 1.6 1 147409 26216 129 144139 1.6 1 121958 22181 130 106601 1.6 1 90012 16589 131 141712 1.6 1 119681 22031 132 71531 1.6 1 60372 11159 133 26436 1.6 1 22268 4168 134 14419 1.6 1 12179 2240 135 4404 1.6 1 3659 745 136 1873 1.6 1 1614 259 137 111 1.6 1 91 20 138 30 1.6 1 24 6 139 10 1.6 1 9 1 140 4 1.6 1 4 141 3 1.6 1 2 1 142 1 1.6 1 1 144 6 1.6 1 2 4 147 8 1.6 1 4 4 148 147 1.6 1 126 21 149 29 1.6 1 26 3 150 560 1.6 1 491 69 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R1_001.fastq.gz ============================================= 109570006 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5866846 (5.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 41006195 (37.4%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1231660) or CGA (54436579) in total: 55668239 (50.8%)