SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_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/Meth14_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 1689.49 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 69,473,196 Reads with adapters: 54,757,002 (78.8%) Reads written (passing filters): 69,473,196 (100.0%) Total basepairs processed: 10,342,355,649 bp Total written (filtered): 7,306,131,783 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 54757002 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.5% C: 2.6% G: 39.4% T: 5.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9197747 17368299.0 0 9197747 2 791126 4342074.8 0 791126 3 650060 1085518.7 0 650060 4 300051 271379.7 0 300051 5 207094 67844.9 0 207094 6 183231 16961.2 0 183231 7 206636 4240.3 0 206636 8 226217 1060.1 0 226217 9 194194 265.0 0 192768 1426 10 239058 66.3 1 221959 17099 11 408625 16.6 1 373369 35256 12 262789 4.1 1 239771 23018 13 214488 1.0 1 191823 22665 14 227214 1.0 1 204150 23064 15 186533 1.0 1 168602 17931 16 210213 1.0 1 188151 22062 17 224535 1.0 1 202585 21950 18 215457 1.0 1 195058 20399 19 241405 1.0 1 218468 22937 20 243924 1.0 1 220366 23558 21 264163 1.0 1 237649 26514 22 264559 1.0 1 239756 24803 23 297505 1.0 1 269472 28033 24 302339 1.0 1 273883 28456 25 298219 1.0 1 270303 27916 26 200126 1.0 1 179911 20215 27 255485 1.0 1 228796 26689 28 406873 1.0 1 371566 35307 29 269701 1.0 1 243338 26363 30 252209 1.0 1 229366 22843 31 259037 1.0 1 234311 24726 32 273918 1.0 1 248477 25441 33 248703 1.0 1 224614 24089 34 260017 1.0 1 236461 23556 35 257033 1.0 1 232060 24973 36 268162 1.0 1 243710 24452 37 339901 1.0 1 308266 31635 38 334547 1.0 1 303634 30913 39 314407 1.0 1 284548 29859 40 443344 1.0 1 403840 39504 41 422616 1.0 1 382612 40004 42 288615 1.0 1 262857 25758 43 319929 1.0 1 290681 29248 44 277603 1.0 1 252069 25534 45 317264 1.0 1 287321 29943 46 342879 1.0 1 309141 33738 47 299956 1.0 1 273661 26295 48 336404 1.0 1 305257 31147 49 553560 1.0 1 503398 50162 50 348651 1.0 1 316232 32419 51 349468 1.0 1 316200 33268 52 436733 1.0 1 395379 41354 53 379569 1.0 1 344088 35481 54 721200 1.0 1 657042 64158 55 342173 1.0 1 309916 32257 56 347373 1.0 1 314411 32962 57 608317 1.0 1 552920 55397 58 367949 1.0 1 332225 35724 59 324979 1.0 1 294257 30722 60 740386 1.0 1 674689 65697 61 382326 1.0 1 346166 36160 62 332142 1.0 1 295077 37065 63 951147 1.0 1 867402 83745 64 272348 1.0 1 245701 26647 65 198937 1.0 1 179459 19478 66 215348 1.0 1 193519 21829 67 572565 1.0 1 521252 51313 68 542463 1.0 1 491631 50832 69 427048 1.0 1 386599 40449 70 618005 1.0 1 560912 57093 71 569054 1.0 1 515913 53141 72 462342 1.0 1 417497 44845 73 941079 1.0 1 855358 85721 74 1301136 1.0 1 1181408 119728 75 406521 1.0 1 367659 38862 76 338564 1.0 1 306385 32179 77 230982 1.0 1 206795 24187 78 267339 1.0 1 241279 26060 79 331027 1.0 1 298842 32185 80 355168 1.0 1 319944 35224 81 309160 1.0 1 278700 30460 82 335140 1.0 1 302340 32800 83 345577 1.0 1 311091 34486 84 464235 1.0 1 418098 46137 85 430740 1.0 1 387769 42971 86 344274 1.0 1 309038 35236 87 409694 1.0 1 368415 41279 88 347765 1.0 1 312880 34885 89 419319 1.0 1 376833 42486 90 402929 1.0 1 362455 40474 91 435170 1.0 1 390938 44232 92 321501 1.0 1 288699 32802 93 375027 1.0 1 336301 38726 94 417103 1.0 1 374154 42949 95 299840 1.0 1 268676 31164 96 322439 1.0 1 288700 33739 97 430709 1.0 1 385800 44909 98 410208 1.0 1 367535 42673 99 371684 1.0 1 332048 39636 100 391758 1.0 1 349967 41791 101 297443 1.0 1 265087 32356 102 290284 1.0 1 258921 31363 103 359954 1.0 1 321158 38796 104 306323 1.0 1 272755 33568 105 298940 1.0 1 266054 32886 106 486818 1.0 1 433188 53630 107 373478 1.0 1 331629 41849 108 383489 1.0 1 341083 42406 109 430389 1.0 1 382372 48017 110 284755 1.0 1 252983 31772 111 284268 1.0 1 252483 31785 112 320100 1.0 1 283685 36415 113 283802 1.0 1 251693 32109 114 472995 1.0 1 418840 54155 115 891460 1.0 1 789541 101919 116 259122 1.0 1 228258 30864 117 361635 1.0 1 318519 43116 118 335624 1.0 1 295770 39854 119 352655 1.0 1 310802 41853 120 201209 1.0 1 176857 24352 121 204289 1.0 1 179728 24561 122 183152 1.0 1 160739 22413 123 199205 1.0 1 174646 24559 124 193647 1.0 1 169805 23842 125 255331 1.0 1 223703 31628 126 153044 1.0 1 133926 19118 127 128172 1.0 1 112200 15972 128 79879 1.0 1 69697 10182 129 63552 1.0 1 55540 8012 130 46254 1.0 1 40233 6021 131 62315 1.0 1 54565 7750 132 28013 1.0 1 24322 3691 133 10585 1.0 1 9135 1450 134 5808 1.0 1 4947 861 135 1598 1.0 1 1368 230 136 684 1.0 1 601 83 137 36 1.0 1 33 3 138 11 1.0 1 10 1 139 7 1.0 1 6 1 140 8 1.0 1 8 141 8 1.0 1 6 2 142 2 1.0 1 1 1 144 2 1.0 1 1 1 145 2 1.0 1 2 147 2 1.0 1 2 148 58 1.0 1 51 7 149 24 1.0 1 20 4 150 289 1.0 1 264 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R2_001.fastq.gz ============================================= 69473196 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7124230 (10.3%) 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 (771107) or CGA (36511320) in total: 37282427 (53.7%) Total number of sequences analysed for the sequence pair length validation: 69473196 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 313337 (0.45%)