SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_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/Meth4_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 3618.83 s (24 us/read; 2.50 M reads/minute). === Summary === Total reads processed: 150,624,528 Reads with adapters: 123,278,388 (81.8%) Reads written (passing filters): 150,624,528 (100.0%) Total basepairs processed: 22,564,820,809 bp Total written (filtered): 15,728,080,367 bp (69.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 123278388 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.3% C: 2.9% G: 44.7% T: 5.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17926941 37656132.0 0 17926941 2 1629060 9414033.0 0 1629060 3 1127081 2353508.2 0 1127081 4 4408237 588377.1 0 4408237 5 507349 147094.3 0 507349 6 409510 36773.6 0 409510 7 436136 9193.4 0 436136 8 402372 2298.3 0 402372 9 371021 574.6 0 365110 5911 10 559431 143.6 1 513570 45861 11 488616 35.9 1 442071 46545 12 503385 9.0 1 455371 48014 13 526794 2.2 1 470871 55923 14 552304 2.2 1 491787 60517 15 674521 2.2 1 603250 71271 16 763387 2.2 1 676764 86623 17 524698 2.2 1 465066 59632 18 549959 2.2 1 492758 57201 19 534333 2.2 1 477885 56448 20 930236 2.2 1 832975 97261 21 563541 2.2 1 501928 61613 22 747074 2.2 1 669031 78043 23 550154 2.2 1 490338 59816 24 573693 2.2 1 507658 66035 25 1011625 2.2 1 904878 106747 26 551110 2.2 1 490832 60278 27 761201 2.2 1 677236 83965 28 2074838 2.2 1 1858685 216153 29 698868 2.2 1 619185 79683 30 634708 2.2 1 567752 66956 31 697946 2.2 1 623660 74286 32 911986 2.2 1 815557 96429 33 620881 2.2 1 551932 68949 34 710617 2.2 1 633940 76677 35 656720 2.2 1 584849 71871 36 604486 2.2 1 534170 70316 37 649973 2.2 1 581767 68206 38 970085 2.2 1 867378 102707 39 737457 2.2 1 657190 80267 40 901784 2.2 1 805308 96476 41 1224543 2.2 1 1092982 131561 42 704106 2.2 1 623714 80392 43 994656 2.2 1 871526 123130 44 952359 2.2 1 841944 110415 45 1141074 2.2 1 1021530 119544 46 543061 2.2 1 480898 62163 47 595940 2.2 1 527957 67983 48 744798 2.2 1 661862 82936 49 805957 2.2 1 718270 87687 50 581810 2.2 1 510966 70844 51 955412 2.2 1 855088 100324 52 643803 2.2 1 568882 74921 53 561556 2.2 1 496265 65291 54 844459 2.2 1 749828 94631 55 985435 2.2 1 875588 109847 56 729733 2.2 1 647451 82282 57 940576 2.2 1 837633 102943 58 1047851 2.2 1 926197 121654 59 1255922 2.2 1 1123839 132083 60 925301 2.2 1 823105 102196 61 835208 2.2 1 740018 95190 62 787102 2.2 1 695244 91858 63 925875 2.2 1 827116 98759 64 750734 2.2 1 665032 85702 65 752704 2.2 1 667155 85549 66 947743 2.2 1 836316 111427 67 776177 2.2 1 686068 90109 68 732667 2.2 1 646315 86352 69 834630 2.2 1 720687 113943 70 2073402 2.2 1 1865772 207630 71 346381 2.2 1 309848 36533 72 88612 2.2 1 76012 12600 73 189138 2.2 1 160288 28850 74 527145 2.2 1 462450 64695 75 706430 2.2 1 624059 82371 76 1099520 2.2 1 971235 128285 77 744676 2.2 1 655670 89006 78 592279 2.2 1 521339 70940 79 808120 2.2 1 712479 95641 80 730827 2.2 1 642344 88483 81 720896 2.2 1 634443 86453 82 951089 2.2 1 836563 114526 83 762900 2.2 1 670404 92496 84 905291 2.2 1 795140 110151 85 933124 2.2 1 816240 116884 86 788744 2.2 1 687756 100988 87 835429 2.2 1 731643 103786 88 1058598 2.2 1 927737 130861 89 961249 2.2 1 841738 119511 90 1105458 2.2 1 968895 136563 91 1119746 2.2 1 980263 139483 92 1016580 2.2 1 888416 128164 93 1014188 2.2 1 885659 128529 94 1175409 2.2 1 1024452 150957 95 826076 2.2 1 718798 107278 96 1292670 2.2 1 1128212 164458 97 1142779 2.2 1 995220 147559 98 1104950 2.2 1 961366 143584 99 955719 2.2 1 830972 124747 100 1014295 2.2 1 881529 132766 101 787403 2.2 1 682689 104714 102 722257 2.2 1 626532 95725 103 951202 2.2 1 825115 126087 104 814717 2.2 1 704603 110114 105 769224 2.2 1 665301 103923 106 948544 2.2 1 820515 128029 107 686527 2.2 1 591875 94652 108 798243 2.2 1 687617 110626 109 870079 2.2 1 747453 122626 110 765858 2.2 1 658273 107585 111 743948 2.2 1 638808 105140 112 1170274 2.2 1 1005227 165047 113 712644 2.2 1 609774 102870 114 913331 2.2 1 781221 132110 115 1064364 2.2 1 911825 152539 116 685707 2.2 1 585330 100377 117 706162 2.2 1 602201 103961 118 1015924 2.2 1 866717 149207 119 1238461 2.2 1 1055942 182519 120 615046 2.2 1 522969 92077 121 672403 2.2 1 571120 101283 122 593766 2.2 1 504215 89551 123 627170 2.2 1 532776 94394 124 711539 2.2 1 604566 106973 125 365643 2.2 1 309999 55644 126 399539 2.2 1 338517 61022 127 548562 2.2 1 465380 83182 128 223311 2.2 1 188582 34729 129 168704 2.2 1 142915 25789 130 149921 2.2 1 126976 22945 131 151895 2.2 1 128658 23237 132 76747 2.2 1 64877 11870 133 29756 2.2 1 25187 4569 134 5398 2.2 1 4590 808 135 1162 2.2 1 939 223 136 1058 2.2 1 881 177 137 83 2.2 1 68 15 138 38 2.2 1 30 8 139 24 2.2 1 23 1 140 16 2.2 1 15 1 141 12 2.2 1 10 2 142 5 2.2 1 3 2 143 3 2.2 1 1 2 144 2 2.2 1 1 1 145 3 2.2 1 3 146 5 2.2 1 5 147 14 2.2 1 9 5 148 211 2.2 1 171 40 149 306 2.2 1 260 46 150 4147 2.2 1 3579 568 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R1_001.fastq.gz ============================================= 150624528 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 9496390 (6.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 61328973 (40.7%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1764891) or CGA (72831693) in total: 74596584 (49.5%)