SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_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; 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_R2_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 3676.96 s (24 us/read; 2.46 M reads/minute). === Summary === Total reads processed: 150,624,528 Reads with adapters: 120,971,047 (80.3%) Reads written (passing filters): 150,624,528 (100.0%) Total basepairs processed: 22,397,138,794 bp Total written (filtered): 15,763,645,799 bp (70.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 120971047 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.9% C: 2.4% G: 45.1% T: 5.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17704778 37656132.0 0 17704778 2 1751103 9414033.0 0 1751103 3 1263294 2353508.2 0 1263294 4 4365421 588377.1 0 4365421 5 508068 147094.3 0 508068 6 402402 36773.6 0 402402 7 410156 9193.4 0 410156 8 410374 2298.3 0 410374 9 353798 574.6 0 350726 3072 10 539760 143.6 1 503994 35766 11 477668 35.9 1 436982 40686 12 532131 9.0 1 487671 44460 13 486822 2.2 1 436506 50316 14 539545 2.2 1 484419 55126 15 639200 2.2 1 577264 61936 16 761846 2.2 1 679999 81847 17 495288 2.2 1 446356 48932 18 507725 2.2 1 461048 46677 19 565907 2.2 1 512127 53780 20 916493 2.2 1 830102 86391 21 526657 2.2 1 474040 52617 22 738304 2.2 1 672767 65537 23 504904 2.2 1 458802 46102 24 563879 2.2 1 510652 53227 25 1056223 2.2 1 961389 94834 26 497243 2.2 1 448937 48306 27 788720 2.2 1 700456 88264 28 1960766 2.2 1 1792799 167967 29 686529 2.2 1 621548 64981 30 617053 2.2 1 563016 54037 31 693488 2.2 1 629748 63740 32 875248 2.2 1 798864 76384 33 612393 2.2 1 554151 58242 34 716742 2.2 1 648612 68130 35 627810 2.2 1 566068 61742 36 583703 2.2 1 530958 52745 37 648382 2.2 1 589829 58553 38 1010711 2.2 1 920975 89736 39 752123 2.2 1 683221 68902 40 845533 2.2 1 772514 73019 41 1180412 2.2 1 1073473 106939 42 682186 2.2 1 622808 59378 43 912325 2.2 1 831696 80629 44 924149 2.2 1 844398 79751 45 912963 2.2 1 829264 83699 46 823104 2.2 1 747224 75880 47 847707 2.2 1 777784 69923 48 475945 2.2 1 432201 43744 49 675107 2.2 1 613943 61164 50 553917 2.2 1 505794 48123 51 507775 2.2 1 460521 47254 52 892849 2.2 1 814507 78342 53 649067 2.2 1 591115 57952 54 935579 2.2 1 856816 78763 55 601790 2.2 1 545633 56157 56 820426 2.2 1 743091 77335 57 1857360 2.2 1 1700456 156904 58 621978 2.2 1 560827 61151 59 708920 2.2 1 641179 67741 60 1741444 2.2 1 1594528 146916 61 967071 2.2 1 881412 85659 62 563156 2.2 1 497672 65484 63 3045739 2.2 1 2793845 251894 64 811007 2.2 1 736692 74315 65 342532 2.2 1 310142 32390 66 439834 2.2 1 392775 47059 67 1275204 2.2 1 1165564 109640 68 579467 2.2 1 526231 53236 69 548629 2.2 1 497301 51328 70 787077 2.2 1 717268 69809 71 582894 2.2 1 530001 52893 72 397882 2.2 1 360012 37870 73 556894 2.2 1 506122 50772 74 464822 2.2 1 420788 44034 75 551862 2.2 1 499878 51984 76 625742 2.2 1 566750 58992 77 442317 2.2 1 400503 41814 78 500512 2.2 1 453768 46744 79 728733 2.2 1 661483 67250 80 679047 2.2 1 614607 64440 81 687573 2.2 1 623341 64232 82 908445 2.2 1 821639 86806 83 788613 2.2 1 711731 76882 84 893243 2.2 1 806888 86355 85 964196 2.2 1 867348 96848 86 784286 2.2 1 702026 82260 87 809792 2.2 1 730495 79297 88 1004633 2.2 1 907807 96826 89 912131 2.2 1 823742 88389 90 1051789 2.2 1 951255 100534 91 1056348 2.2 1 953368 102980 92 961691 2.2 1 867792 93899 93 963799 2.2 1 870026 93773 94 1101267 2.2 1 990532 110735 95 785924 2.2 1 707576 78348 96 1220856 2.2 1 1100359 120497 97 1090480 2.2 1 981335 109145 98 1066093 2.2 1 960124 105969 99 942920 2.2 1 848644 94276 100 990754 2.2 1 890669 100085 101 756926 2.2 1 679074 77852 102 686249 2.2 1 615696 70553 103 893629 2.2 1 802176 91453 104 761610 2.2 1 682225 79385 105 729367 2.2 1 652853 76514 106 892685 2.2 1 799804 92881 107 653036 2.2 1 584237 68799 108 761204 2.2 1 680292 80912 109 819521 2.2 1 730935 88586 110 726323 2.2 1 647765 78558 111 723001 2.2 1 644213 78788 112 1128978 2.2 1 1005814 123164 113 707572 2.2 1 629023 78549 114 895709 2.2 1 795691 100018 115 1014650 2.2 1 901547 113103 116 660820 2.2 1 586918 73902 117 679832 2.2 1 602661 77171 118 986966 2.2 1 874932 112034 119 1188741 2.2 1 1053713 135028 120 596497 2.2 1 527773 68724 121 649928 2.2 1 575276 74652 122 567927 2.2 1 501179 66748 123 604361 2.2 1 534320 70041 124 683263 2.2 1 603279 79984 125 358064 2.2 1 316245 41819 126 391821 2.2 1 345278 46543 127 528991 2.2 1 466161 62830 128 217432 2.2 1 191228 26204 129 162497 2.2 1 142759 19738 130 145048 2.2 1 127349 17699 131 145578 2.2 1 127871 17707 132 73729 2.2 1 64689 9040 133 28631 2.2 1 25101 3530 134 5200 2.2 1 4565 635 135 1120 2.2 1 966 154 136 1060 2.2 1 904 156 137 74 2.2 1 69 5 138 34 2.2 1 33 1 139 24 2.2 1 17 7 140 19 2.2 1 18 1 141 13 2.2 1 7 6 142 9 2.2 1 5 4 143 1 2.2 1 1 144 2 2.2 1 0 2 145 3 2.2 1 3 146 7 2.2 1 4 3 147 13 2.2 1 9 4 148 193 2.2 1 164 29 149 311 2.2 1 266 45 150 3931 2.2 1 3534 397 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R2_001.fastq.gz ============================================= 150624528 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 17381248 (11.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1609237) or CGA (67354262) in total: 68963499 (45.8%) Total number of sequences analysed for the sequence pair length validation: 150624528 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 795739 (0.53%)