SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_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/20200306/FASTQC 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/20200306/Meth13_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 2649.32 s (26 us/read; 2.29 M reads/minute). === Summary === Total reads processed: 100,994,125 Reads with adapters: 74,282,317 (73.6%) Reads written (passing filters): 100,994,125 (100.0%) Total basepairs processed: 15,032,743,669 bp Total written (filtered): 11,294,465,516 bp (75.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 74282317 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.4% C: 3.1% G: 42.4% T: 8.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16858905 25248531.2 0 16858905 2 1409178 6312132.8 0 1409178 3 1022247 1578033.2 0 1022247 4 449685 394508.3 0 449685 5 282584 98627.1 0 282584 6 231575 24656.8 0 231575 7 275852 6164.2 0 275852 8 305134 1541.0 0 305134 9 261671 385.3 0 259774 1897 10 318513 96.3 1 293638 24875 11 567085 24.1 1 515255 51830 12 364336 6.0 1 330294 34042 13 290786 1.5 1 258428 32358 14 303138 1.5 1 270634 32504 15 246093 1.5 1 220948 25145 16 285123 1.5 1 253722 31401 17 284664 1.5 1 255137 29527 18 286469 1.5 1 258114 28355 19 308210 1.5 1 277962 30248 20 324953 1.5 1 291571 33382 21 303171 1.5 1 270805 32366 22 350374 1.5 1 316862 33512 23 396907 1.5 1 358066 38841 24 381124 1.5 1 343563 37561 25 381056 1.5 1 343740 37316 26 245479 1.5 1 220057 25422 27 291422 1.5 1 259208 32214 28 487231 1.5 1 443161 44070 29 347094 1.5 1 312544 34550 30 331761 1.5 1 300206 31555 31 338587 1.5 1 306037 32550 32 358592 1.5 1 324285 34307 33 314593 1.5 1 283789 30804 34 342874 1.5 1 309361 33513 35 336170 1.5 1 304544 31626 36 344386 1.5 1 308783 35603 37 415065 1.5 1 375228 39837 38 459882 1.5 1 415569 44313 39 404887 1.5 1 365056 39831 40 571974 1.5 1 518878 53096 41 505738 1.5 1 457619 48119 42 365004 1.5 1 331197 33807 43 413898 1.5 1 374763 39135 44 357178 1.5 1 323405 33773 45 457513 1.5 1 412411 45102 46 435158 1.5 1 391388 43770 47 457055 1.5 1 415593 41462 48 395224 1.5 1 357064 38160 49 674244 1.5 1 611485 62759 50 434007 1.5 1 393088 40919 51 427500 1.5 1 385958 41542 52 527271 1.5 1 477474 49797 53 471108 1.5 1 426085 45023 54 923952 1.5 1 841152 82800 55 367371 1.5 1 332096 35275 56 430114 1.5 1 387358 42756 57 935761 1.5 1 849893 85868 58 412305 1.5 1 370915 41390 59 386265 1.5 1 348305 37960 60 1040895 1.5 1 947342 93553 61 455365 1.5 1 412374 42991 62 358198 1.5 1 316355 41843 63 1602264 1.5 1 1461599 140665 64 380614 1.5 1 342988 37626 65 211938 1.5 1 190908 21030 66 250630 1.5 1 223979 26651 67 816496 1.5 1 742960 73536 68 606413 1.5 1 549483 56930 69 513297 1.5 1 464468 48829 70 778232 1.5 1 706072 72160 71 638686 1.5 1 578942 59744 72 481606 1.5 1 435034 46572 73 985078 1.5 1 894565 90513 74 1294627 1.5 1 1176076 118551 75 402361 1.5 1 363629 38732 76 367554 1.5 1 332914 34640 77 298809 1.5 1 267530 31279 78 347369 1.5 1 313518 33851 79 412815 1.5 1 372637 40178 80 429933 1.5 1 387774 42159 81 384917 1.5 1 347266 37651 82 421423 1.5 1 380392 41031 83 424394 1.5 1 382335 42059 84 551836 1.5 1 497555 54281 85 529303 1.5 1 476883 52420 86 424156 1.5 1 381288 42868 87 432689 1.5 1 389037 43652 88 428451 1.5 1 385513 42938 89 518280 1.5 1 466734 51546 90 480143 1.5 1 432447 47696 91 534963 1.5 1 481319 53644 92 359938 1.5 1 323524 36414 93 478512 1.5 1 430743 47769 94 513875 1.5 1 462209 51666 95 371059 1.5 1 333246 37813 96 402062 1.5 1 361080 40982 97 514433 1.5 1 461861 52572 98 516253 1.5 1 463634 52619 99 484360 1.5 1 434891 49469 100 492619 1.5 1 440850 51769 101 379216 1.5 1 339118 40098 102 367605 1.5 1 329106 38499 103 441408 1.5 1 394943 46465 104 386261 1.5 1 345006 41255 105 380001 1.5 1 339706 40295 106 591703 1.5 1 528612 63091 107 472566 1.5 1 421694 50872 108 474327 1.5 1 422729 51598 109 522002 1.5 1 466969 55033 110 362933 1.5 1 323370 39563 111 347657 1.5 1 309474 38183 112 388527 1.5 1 345990 42537 113 339670 1.5 1 302340 37330 114 591254 1.5 1 526319 64935 115 1088418 1.5 1 968434 119984 116 319102 1.5 1 283133 35969 117 434552 1.5 1 386087 48465 118 390585 1.5 1 345582 45003 119 434222 1.5 1 384929 49293 120 249611 1.5 1 221221 28390 121 250773 1.5 1 222295 28478 122 229186 1.5 1 202720 26466 123 241833 1.5 1 213756 28077 124 232011 1.5 1 205157 26854 125 312472 1.5 1 276186 36286 126 178172 1.5 1 157076 21096 127 143853 1.5 1 126656 17197 128 91075 1.5 1 80088 10987 129 73099 1.5 1 64502 8597 130 55464 1.5 1 48732 6732 131 71783 1.5 1 63274 8509 132 30986 1.5 1 27253 3733 133 10709 1.5 1 9385 1324 134 4811 1.5 1 4208 603 135 1166 1.5 1 1010 156 136 476 1.5 1 425 51 137 53 1.5 1 50 3 138 11 1.5 1 8 3 139 8 1.5 1 8 140 6 1.5 1 6 141 6 1.5 1 5 1 142 1 1.5 1 1 143 1 1.5 1 1 145 1 1.5 1 1 146 1 1.5 1 1 148 83 1.5 1 78 5 149 11 1.5 1 10 1 150 304 1.5 1 276 28 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R2_001.fastq.gz ============================================= 100994125 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 11269639 (11.2%) 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 (1082919) or CGA (46567288) in total: 47650207 (47.2%) Total number of sequences analysed for the sequence pair length validation: 100994125 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 386198 (0.38%)