SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_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/Meth6_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 3425.33 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 141,156,454 Reads with adapters: 113,837,190 (80.6%) Reads written (passing filters): 141,156,454 (100.0%) Total basepairs processed: 21,153,231,163 bp Total written (filtered): 14,777,295,273 bp (69.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 113837190 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.0% C: 2.9% G: 43.5% T: 5.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18114339 35289113.5 0 18114339 2 1574373 8822278.4 0 1574373 3 1007754 2205569.6 0 1007754 4 4250018 551392.4 0 4250018 5 442302 137848.1 0 442302 6 347762 34462.0 0 347762 7 365334 8615.5 0 365334 8 340357 2153.9 0 340357 9 315482 538.5 0 310640 4842 10 471633 134.6 1 433478 38155 11 421663 33.7 1 382044 39619 12 434916 8.4 1 394292 40624 13 438923 2.1 1 393185 45738 14 471028 2.1 1 419073 51955 15 588334 2.1 1 527038 61296 16 659216 2.1 1 584462 74754 17 442242 2.1 1 392690 49552 18 464738 2.1 1 417189 47549 19 447764 2.1 1 401135 46629 20 789970 2.1 1 708475 81495 21 480558 2.1 1 429131 51427 22 635929 2.1 1 571408 64521 23 458058 2.1 1 409657 48401 24 482611 2.1 1 427382 55229 25 876414 2.1 1 785434 90980 26 460939 2.1 1 412215 48724 27 658626 2.1 1 587078 71548 28 1799758 2.1 1 1615498 184260 29 585850 2.1 1 520236 65614 30 529463 2.1 1 475005 54458 31 585282 2.1 1 523720 61562 32 791339 2.1 1 709838 81501 33 523884 2.1 1 464846 59038 34 614228 2.1 1 548103 66125 35 503259 2.1 1 451141 52118 36 518785 2.1 1 462642 56143 37 577418 2.1 1 516472 60946 38 829171 2.1 1 742766 86405 39 598228 2.1 1 536212 62016 40 771221 2.1 1 689855 81366 41 1007719 2.1 1 902199 105520 42 651096 2.1 1 579895 71201 43 810589 2.1 1 718318 92271 44 815704 2.1 1 726364 89340 45 873113 2.1 1 783105 90008 46 555823 2.1 1 496558 59265 47 497466 2.1 1 443750 53716 48 536018 2.1 1 478412 57606 49 706414 2.1 1 631817 74597 50 462296 2.1 1 409859 52437 51 553201 2.1 1 492675 60526 52 747148 2.1 1 667860 79288 53 584687 2.1 1 520990 63697 54 594976 2.1 1 528661 66315 55 807010 2.1 1 720703 86307 56 617385 2.1 1 549783 67602 57 664943 2.1 1 592087 72856 58 1049360 2.1 1 936792 112568 59 788797 2.1 1 701914 86883 60 1032253 2.1 1 923344 108909 61 924201 2.1 1 825200 99001 62 665287 2.1 1 592754 72533 63 646590 2.1 1 576969 69621 64 904196 2.1 1 807939 96257 65 600971 2.1 1 533159 67812 66 804852 2.1 1 713102 91750 67 834196 2.1 1 740599 93597 68 704606 2.1 1 624292 80314 69 737201 2.1 1 639979 97222 70 1835471 2.1 1 1659177 176294 71 146239 2.1 1 128480 17759 72 51812 2.1 1 42369 9443 73 266751 2.1 1 231764 34987 74 527827 2.1 1 467912 59915 75 640957 2.1 1 568727 72230 76 991456 2.1 1 881059 110397 77 661610 2.1 1 587359 74251 78 524422 2.1 1 463885 60537 79 724671 2.1 1 642981 81690 80 665056 2.1 1 587670 77386 81 651505 2.1 1 577184 74321 82 848683 2.1 1 750901 97782 83 700372 2.1 1 618164 82208 84 837584 2.1 1 740385 97199 85 867679 2.1 1 761382 106297 86 716477 2.1 1 627596 88881 87 757725 2.1 1 668461 89264 88 966584 2.1 1 853364 113220 89 886376 2.1 1 781501 104875 90 1083017 2.1 1 956205 126812 91 1029811 2.1 1 908183 121628 92 969446 2.1 1 853993 115453 93 946417 2.1 1 832660 113757 94 1108732 2.1 1 973513 135219 95 788984 2.1 1 693000 95984 96 1236749 2.1 1 1088116 148633 97 1103594 2.1 1 969080 134514 98 1044148 2.1 1 916235 127913 99 893180 2.1 1 783603 109577 100 949568 2.1 1 832494 117074 101 757207 2.1 1 661462 95745 102 683926 2.1 1 597480 86446 103 951775 2.1 1 834069 117706 104 782437 2.1 1 683548 98889 105 739176 2.1 1 646051 93125 106 906327 2.1 1 791325 115002 107 662894 2.1 1 576957 85937 108 785037 2.1 1 683425 101612 109 844550 2.1 1 733461 111089 110 744513 2.1 1 646804 97709 111 723492 2.1 1 627629 95863 112 1135938 2.1 1 987053 148885 113 702661 2.1 1 607906 94755 114 912212 2.1 1 789279 122933 115 1072461 2.1 1 929016 143445 116 695792 2.1 1 600051 95741 117 707423 2.1 1 610644 96779 118 1029503 2.1 1 889552 139951 119 1348020 2.1 1 1163691 184329 120 649575 2.1 1 558317 91258 121 663434 2.1 1 570732 92702 122 594253 2.1 1 511395 82858 123 644630 2.1 1 555455 89175 124 698142 2.1 1 600164 97978 125 361771 2.1 1 310176 51595 126 400106 2.1 1 343199 56907 127 566043 2.1 1 485840 80203 128 223004 2.1 1 191159 31845 129 163989 2.1 1 140469 23520 130 146798 2.1 1 125751 21047 131 152862 2.1 1 130878 21984 132 76554 2.1 1 65612 10942 133 28647 2.1 1 24708 3939 134 5546 2.1 1 4770 776 135 1233 2.1 1 1031 202 136 1363 2.1 1 1190 173 137 103 2.1 1 90 13 138 27 2.1 1 22 5 139 26 2.1 1 22 4 140 14 2.1 1 3 11 141 5 2.1 1 5 142 5 2.1 1 3 2 143 4 2.1 1 4 144 6 2.1 1 6 145 1 2.1 1 0 1 146 5 2.1 1 3 2 147 4 2.1 1 2 2 148 134 2.1 1 111 23 149 204 2.1 1 172 32 150 3188 2.1 1 2733 455 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R1_001.fastq.gz ============================================= 141156454 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 6247628 (4.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 55045586 (39.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1680815) or CGA (69814672) in total: 71495487 (50.6%)