SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_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/Meth15_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 2732.35 s (25 us/read; 2.41 M reads/minute). === Summary === Total reads processed: 109,570,006 Reads with adapters: 83,811,500 (76.5%) Reads written (passing filters): 109,570,006 (100.0%) Total basepairs processed: 16,277,955,576 bp Total written (filtered): 11,729,149,239 bp (72.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 83811500 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 2.6% G: 44.4% T: 6.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15643604 27392501.5 0 15643604 2 1404461 6848125.4 0 1404461 3 1032068 1712031.3 0 1032068 4 495162 428007.8 0 495162 5 315265 107002.0 0 315265 6 281806 26750.5 0 281806 7 315056 6687.6 0 315056 8 343362 1671.9 0 343362 9 303966 418.0 0 301786 2180 10 364458 104.5 1 337350 27108 11 636950 26.1 1 577475 59475 12 415500 6.5 1 378195 37305 13 327101 1.6 1 291246 35855 14 334728 1.6 1 300065 34663 15 293162 1.6 1 262741 30421 16 333254 1.6 1 297273 35981 17 328131 1.6 1 295009 33122 18 321080 1.6 1 289708 31372 19 382369 1.6 1 344782 37587 20 357602 1.6 1 321903 35699 21 333890 1.6 1 299589 34301 22 403737 1.6 1 364438 39299 23 495561 1.6 1 447621 47940 24 430568 1.6 1 388613 41955 25 435718 1.6 1 393815 41903 26 279865 1.6 1 251513 28352 27 353301 1.6 1 315930 37371 28 569412 1.6 1 518365 51047 29 386976 1.6 1 347737 39239 30 361508 1.6 1 327534 33974 31 384181 1.6 1 345906 38275 32 398982 1.6 1 361474 37508 33 378366 1.6 1 340059 38307 34 422614 1.6 1 382314 40300 35 367792 1.6 1 332596 35196 36 403291 1.6 1 361515 41776 37 529705 1.6 1 478848 50857 38 528089 1.6 1 472928 55161 39 511744 1.6 1 457170 54574 40 641148 1.6 1 582863 58285 41 597201 1.6 1 539426 57775 42 443261 1.6 1 402607 40654 43 432281 1.6 1 390543 41738 44 452376 1.6 1 409941 42435 45 537153 1.6 1 484438 52715 46 510405 1.6 1 458984 51421 47 700998 1.6 1 639352 61646 48 312850 1.6 1 281030 31820 49 724516 1.6 1 656801 67715 50 504634 1.6 1 457939 46695 51 433338 1.6 1 390768 42570 52 619613 1.6 1 560502 59111 53 524596 1.6 1 472405 52191 54 1164400 1.6 1 1061414 102986 55 336683 1.6 1 302509 34174 56 506802 1.6 1 452593 54209 57 1713467 1.6 1 1562674 150793 58 380124 1.6 1 339541 40583 59 350769 1.6 1 312681 38088 60 1486641 1.6 1 1353823 132818 61 474221 1.6 1 428726 45495 62 389291 1.6 1 339128 50163 63 2403019 1.6 1 2192515 210504 64 664617 1.6 1 603401 61216 65 209309 1.6 1 187984 21325 66 259805 1.6 1 230002 29803 67 1021196 1.6 1 929011 92185 68 556813 1.6 1 502779 54034 69 498388 1.6 1 449011 49377 70 799861 1.6 1 725414 74447 71 549560 1.6 1 496408 53152 72 431189 1.6 1 387803 43386 73 912672 1.6 1 825986 86686 74 1215964 1.6 1 1101520 114444 75 387223 1.6 1 348654 38569 76 439150 1.6 1 397016 42134 77 308592 1.6 1 275729 32863 78 390003 1.6 1 351604 38399 79 465817 1.6 1 419820 45997 80 500520 1.6 1 450662 49858 81 439923 1.6 1 395631 44292 82 486249 1.6 1 437371 48878 83 499883 1.6 1 449436 50447 84 685820 1.6 1 616711 69109 85 633416 1.6 1 568645 64771 86 491581 1.6 1 440530 51051 87 556922 1.6 1 499982 56940 88 500754 1.6 1 450100 50654 89 600638 1.6 1 539777 60861 90 567327 1.6 1 509781 57546 91 639615 1.6 1 574511 65104 92 449676 1.6 1 403204 46472 93 555974 1.6 1 499491 56483 94 618669 1.6 1 555245 63424 95 428774 1.6 1 383862 44912 96 464401 1.6 1 416024 48377 97 609349 1.6 1 545451 63898 98 599249 1.6 1 536342 62907 99 546292 1.6 1 488390 57902 100 600200 1.6 1 535861 64339 101 463544 1.6 1 413256 50288 102 447382 1.6 1 398994 48388 103 527840 1.6 1 471266 56574 104 466116 1.6 1 415619 50497 105 457490 1.6 1 407507 49983 106 729732 1.6 1 649934 79798 107 586569 1.6 1 521881 64688 108 585355 1.6 1 520142 65213 109 655586 1.6 1 582992 72594 110 445079 1.6 1 395391 49688 111 423064 1.6 1 375407 47657 112 491877 1.6 1 436210 55667 113 426838 1.6 1 377878 48960 114 718856 1.6 1 636056 82800 115 1343866 1.6 1 1190996 152870 116 433588 1.6 1 383499 50089 117 562583 1.6 1 496034 66549 118 564042 1.6 1 497114 66928 119 608898 1.6 1 537036 71862 120 345174 1.6 1 303547 41627 121 358548 1.6 1 315632 42916 122 324348 1.6 1 284899 39449 123 363526 1.6 1 319323 44203 124 366908 1.6 1 322053 44855 125 475676 1.6 1 416659 59017 126 294723 1.6 1 258353 36370 127 256017 1.6 1 224163 31854 128 168906 1.6 1 147377 21529 129 138126 1.6 1 120620 17506 130 102655 1.6 1 89603 13052 131 134692 1.6 1 117223 17469 132 68185 1.6 1 59411 8774 133 25423 1.6 1 21912 3511 134 13817 1.6 1 11938 1879 135 4221 1.6 1 3660 561 136 1815 1.6 1 1547 268 137 97 1.6 1 82 15 138 26 1.6 1 25 1 139 9 1.6 1 8 1 140 6 1.6 1 6 141 3 1.6 1 3 142 3 1.6 1 0 3 144 6 1.6 1 2 4 145 1 1.6 1 0 1 146 1 1.6 1 0 1 147 3 1.6 1 3 148 145 1.6 1 129 16 149 30 1.6 1 21 9 150 542 1.6 1 498 44 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R2_001.fastq.gz ============================================= 109570006 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 14718642 (13.4%) 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 (1128168) or CGA (49375162) in total: 50503330 (46.1%) Total number of sequences analysed for the sequence pair length validation: 109570006 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 658759 (0.60%)