SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_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/Meth6_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 3476.60 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 141,156,454 Reads with adapters: 111,733,219 (79.2%) Reads written (passing filters): 141,156,454 (100.0%) Total basepairs processed: 20,979,423,224 bp Total written (filtered): 14,812,856,951 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 111733219 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 2.4% G: 45.9% T: 6.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17858932 35289113.5 0 17858932 2 1685175 8822278.4 0 1685175 3 1124401 2205569.6 0 1124401 4 4220919 551392.4 0 4220919 5 443848 137848.1 0 443848 6 341360 34462.0 0 341360 7 342952 8615.5 0 342952 8 356623 2153.9 0 356623 9 290110 538.5 0 287583 2527 10 454777 134.6 1 421576 33201 11 413253 33.7 1 375286 37967 12 456190 8.4 1 415576 40614 13 408256 2.1 1 363113 45143 14 459736 2.1 1 409896 49840 15 559389 2.1 1 503284 56105 16 655958 2.1 1 582534 73424 17 421067 2.1 1 377065 44002 18 425463 2.1 1 384800 40663 19 482623 2.1 1 434178 48445 20 779305 2.1 1 703755 75550 21 440291 2.1 1 394388 45903 22 627676 2.1 1 569224 58452 23 422073 2.1 1 382010 40063 24 503775 2.1 1 452738 51037 25 937725 2.1 1 851371 86354 26 402134 2.1 1 360990 41144 27 624215 2.1 1 552281 71934 28 1731891 2.1 1 1578669 153222 29 570079 2.1 1 514473 55606 30 530485 2.1 1 481756 48729 31 567254 2.1 1 514197 53057 32 776163 2.1 1 705291 70872 33 504872 2.1 1 455882 48990 34 592287 2.1 1 537595 54692 35 561574 2.1 1 509203 52371 36 482695 2.1 1 437276 45419 37 522907 2.1 1 471859 51048 38 828973 2.1 1 754521 74452 39 642886 2.1 1 583250 59636 40 721153 2.1 1 650973 70180 41 991611 2.1 1 902072 89539 42 605436 2.1 1 550101 55335 43 791018 2.1 1 716693 74325 44 1159234 2.1 1 1054627 104607 45 898926 2.1 1 814064 84862 46 699793 2.1 1 634958 64835 47 684835 2.1 1 626890 57945 48 243094 2.1 1 217758 25336 49 630998 2.1 1 574754 56244 50 425578 2.1 1 387204 38374 51 404356 2.1 1 366658 37698 52 727803 2.1 1 663712 64091 53 543965 2.1 1 494058 49907 54 953452 2.1 1 874691 78761 55 373643 2.1 1 336354 37289 56 661450 2.1 1 593000 68450 57 2364263 2.1 1 2168267 195996 58 478801 2.1 1 430071 48730 59 458217 2.1 1 411353 46864 60 1717820 2.1 1 1572953 144867 61 696246 2.1 1 633874 62372 62 560955 2.1 1 498886 62069 63 2435828 2.1 1 2234061 201767 64 1034971 2.1 1 943304 91667 65 226288 2.1 1 203628 22660 66 376835 2.1 1 337545 39290 67 954911 2.1 1 873694 81217 68 412791 2.1 1 375565 37226 69 325391 2.1 1 294251 31140 70 591408 2.1 1 540495 50913 71 335944 2.1 1 305764 30180 72 308894 2.1 1 279852 29042 73 480128 2.1 1 436832 43296 74 476667 2.1 1 432947 43720 75 570273 2.1 1 518524 51749 76 628946 2.1 1 574175 54771 77 244084 2.1 1 219063 25021 78 379810 2.1 1 344178 35632 79 624782 2.1 1 566778 58004 80 610404 2.1 1 551758 58646 81 620049 2.1 1 561932 58117 82 815011 2.1 1 737990 77021 83 738729 2.1 1 667051 71678 84 834801 2.1 1 754060 80741 85 915295 2.1 1 822073 93222 86 727156 2.1 1 650738 76418 87 743126 2.1 1 670270 72856 88 928181 2.1 1 839185 88996 89 847306 2.1 1 767044 80262 90 1031875 2.1 1 933919 97956 91 973712 2.1 1 879276 94436 92 918932 2.1 1 831550 87382 93 902762 2.1 1 816499 86263 94 1040450 2.1 1 937478 102972 95 752249 2.1 1 679003 73246 96 1168688 2.1 1 1055805 112883 97 1054965 2.1 1 953091 101874 98 1007282 2.1 1 909349 97933 99 883508 2.1 1 796332 87176 100 929808 2.1 1 838918 90890 101 730503 2.1 1 657472 73031 102 652090 2.1 1 587111 64979 103 895396 2.1 1 807211 88185 104 732440 2.1 1 658599 73841 105 701726 2.1 1 630831 70895 106 853741 2.1 1 767751 85990 107 631935 2.1 1 567318 64617 108 751248 2.1 1 674879 76369 109 803270 2.1 1 719722 83548 110 715468 2.1 1 641478 73990 111 703844 2.1 1 630306 73538 112 1085719 2.1 1 972938 112781 113 669719 2.1 1 598176 71543 114 865811 2.1 1 773438 92373 115 1006313 2.1 1 899665 106648 116 663558 2.1 1 592333 71225 117 680402 2.1 1 606877 73525 118 999647 2.1 1 892258 107389 119 1296038 2.1 1 1155443 140595 120 630947 2.1 1 562461 68486 121 642203 2.1 1 572254 69949 122 568797 2.1 1 505376 63421 123 621348 2.1 1 552761 68587 124 669349 2.1 1 595229 74120 125 354144 2.1 1 314752 39392 126 392385 2.1 1 348863 43522 127 545238 2.1 1 484293 60945 128 216795 2.1 1 192329 24466 129 157673 2.1 1 139757 17916 130 141932 2.1 1 126177 15755 131 146108 2.1 1 129591 16517 132 73370 2.1 1 65100 8270 133 27488 2.1 1 24402 3086 134 5301 2.1 1 4663 638 135 1186 2.1 1 1031 155 136 1359 2.1 1 1160 199 137 100 2.1 1 93 7 138 27 2.1 1 25 2 139 25 2.1 1 22 3 140 18 2.1 1 17 1 141 7 2.1 1 7 142 6 2.1 1 4 2 143 4 2.1 1 4 144 4 2.1 1 4 146 8 2.1 1 6 2 147 5 2.1 1 4 1 148 138 2.1 1 115 23 149 205 2.1 1 188 17 150 3002 2.1 1 2719 283 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R2_001.fastq.gz ============================================= 141156454 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 18064917 (12.8%) 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 (1486804) or CGA (62519750) in total: 64006554 (45.3%) Total number of sequences analysed for the sequence pair length validation: 141156454 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 774349 (0.55%)