SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_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; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/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 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R1_001.fastq.gz 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 2515.36 s (30 us/read; 2.01 M reads/minute). === Summary === Total reads processed: 84,066,692 Reads with adapters: 53,982,918 (64.2%) Reads written (passing filters): 84,066,692 (100.0%) Total basepairs processed: 12,610,003,800 bp Quality-trimmed: 20,918,384 bp (0.2%) Total written (filtered): 10,867,974,302 bp (86.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 53982918 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.6% C: 19.5% G: 16.0% T: 28.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18241553 21016673.0 0 18241553 2 1862687 5254168.2 0 1862687 3 833046 1313542.1 0 833046 4 516579 328385.5 0 516579 5 391725 82096.4 0 391725 6 321578 20524.1 0 321578 7 339416 5131.0 0 339416 8 364811 1282.8 0 364811 9 342163 320.7 0 331139 11024 10 366956 80.2 1 336869 30087 11 386092 20.0 1 350781 35311 12 388598 5.0 1 355892 32706 13 372333 1.3 1 339080 33253 14 379847 1.3 1 343961 35886 15 380756 1.3 1 346533 34223 16 389402 1.3 1 353476 35926 17 397244 1.3 1 360847 36397 18 378093 1.3 1 345267 32826 19 373706 1.3 1 339971 33735 20 384835 1.3 1 350873 33962 21 389517 1.3 1 354181 35336 22 385354 1.3 1 351056 34298 23 394576 1.3 1 359374 35202 24 383165 1.3 1 346880 36285 25 389063 1.3 1 355061 34002 26 386488 1.3 1 352699 33789 27 394205 1.3 1 359008 35197 28 387219 1.3 1 354631 32588 29 386534 1.3 1 353495 33039 30 385582 1.3 1 354878 30704 31 378741 1.3 1 348477 30264 32 381496 1.3 1 350881 30615 33 380078 1.3 1 348170 31908 34 386598 1.3 1 353100 33498 35 437824 1.3 1 406428 31396 36 319589 1.3 1 291939 27650 37 386294 1.3 1 354201 32093 38 387420 1.3 1 357234 30186 39 377276 1.3 1 344190 33086 40 380004 1.3 1 349514 30490 41 378400 1.3 1 346411 31989 42 368715 1.3 1 339028 29687 43 393263 1.3 1 359333 33930 44 371321 1.3 1 337007 34314 45 492350 1.3 1 459797 32553 46 247208 1.3 1 223670 23538 47 360607 1.3 1 331388 29219 48 371474 1.3 1 341636 29838 49 364728 1.3 1 335604 29124 50 356549 1.3 1 326287 30262 51 376963 1.3 1 345079 31884 52 356425 1.3 1 328020 28405 53 338455 1.3 1 310191 28264 54 350556 1.3 1 321230 29326 55 357130 1.3 1 328622 28508 56 339762 1.3 1 311807 27955 57 348990 1.3 1 319578 29412 58 363847 1.3 1 334763 29084 59 321036 1.3 1 292991 28045 60 330539 1.3 1 304298 26241 61 316332 1.3 1 289897 26435 62 330822 1.3 1 303274 27548 63 336876 1.3 1 309013 27863 64 323007 1.3 1 297091 25916 65 285363 1.3 1 258734 26629 66 337137 1.3 1 307329 29808 67 354167 1.3 1 322051 32116 68 376537 1.3 1 344529 32008 69 366041 1.3 1 322871 43170 70 685429 1.3 1 647559 37870 71 58912 1.3 1 53673 5239 72 41160 1.3 1 34454 6706 73 142719 1.3 1 127267 15452 74 228335 1.3 1 207761 20574 75 248506 1.3 1 226185 22321 76 250348 1.3 1 228177 22171 77 246047 1.3 1 224038 22009 78 241776 1.3 1 219577 22199 79 240909 1.3 1 219225 21684 80 230041 1.3 1 209163 20878 81 227283 1.3 1 206367 20916 82 224775 1.3 1 203770 21005 83 219042 1.3 1 199636 19406 84 211949 1.3 1 193324 18625 85 206705 1.3 1 187417 19288 86 198070 1.3 1 179511 18559 87 196394 1.3 1 178172 18222 88 172375 1.3 1 155263 17112 89 164349 1.3 1 147287 17062 90 161509 1.3 1 144701 16808 91 159887 1.3 1 143250 16637 92 152138 1.3 1 136692 15446 93 144742 1.3 1 129919 14823 94 143351 1.3 1 128852 14499 95 137554 1.3 1 123193 14361 96 128515 1.3 1 115058 13457 97 123948 1.3 1 110847 13101 98 113273 1.3 1 100799 12474 99 107803 1.3 1 95518 12285 100 103457 1.3 1 91768 11689 101 102113 1.3 1 90487 11626 102 91930 1.3 1 80734 11196 103 88109 1.3 1 77683 10426 104 91171 1.3 1 80503 10668 105 87463 1.3 1 76891 10572 106 87859 1.3 1 77315 10544 107 81281 1.3 1 71246 10035 108 70347 1.3 1 61624 8723 109 61615 1.3 1 53343 8272 110 58115 1.3 1 50285 7830 111 53031 1.3 1 45317 7714 112 49720 1.3 1 42849 6871 113 49878 1.3 1 43367 6511 114 47224 1.3 1 41140 6084 115 45098 1.3 1 39294 5804 116 46676 1.3 1 40888 5788 117 48959 1.3 1 43067 5892 118 41255 1.3 1 36147 5108 119 35910 1.3 1 31626 4284 120 32932 1.3 1 28993 3939 121 28575 1.3 1 24860 3715 122 33533 1.3 1 29452 4081 123 33378 1.3 1 29388 3990 124 28827 1.3 1 25348 3479 125 28718 1.3 1 24934 3784 126 56698 1.3 1 49735 6963 127 45176 1.3 1 39337 5839 128 23455 1.3 1 20403 3052 129 25227 1.3 1 22368 2859 130 61584 1.3 1 56091 5493 131 122842 1.3 1 115925 6917 132 131126 1.3 1 122965 8161 133 213119 1.3 1 200231 12888 134 221596 1.3 1 207188 14408 135 55160 1.3 1 50811 4349 136 14830 1.3 1 12995 1835 137 9504 1.3 1 8070 1434 138 7082 1.3 1 5656 1426 139 3894 1.3 1 2975 919 140 3420 1.3 1 2419 1001 141 1329 1.3 1 915 414 142 970 1.3 1 580 390 143 793 1.3 1 605 188 144 1547 1.3 1 1288 259 145 5321 1.3 1 4709 612 146 9538 1.3 1 8221 1317 147 81394 1.3 1 70126 11268 148 44121 1.3 1 36994 7127 149 12986 1.3 1 11079 1907 150 172145 1.3 1 154799 17346 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R1_001.fastq.gz ============================================= 84066692 sequences processed in total