SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_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; 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/Meth3_R2_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 2483.85 s (32 us/read; 1.89 M reads/minute). === Summary === Total reads processed: 78,207,503 Reads with adapters: 49,568,577 (63.4%) Reads written (passing filters): 78,207,503 (100.0%) Total basepairs processed: 11,731,125,450 bp Quality-trimmed: 89,899,767 bp (0.8%) Total written (filtered): 10,460,935,613 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 49568577 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.9% C: 12.8% G: 18.2% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18539356 19551875.8 0 18539356 2 1849311 4887968.9 0 1849311 3 944620 1221992.2 0 944620 4 578894 305498.1 0 578894 5 422973 76374.5 0 422973 6 345562 19093.6 0 345562 7 358049 4773.4 0 358049 8 411077 1193.4 0 411077 9 362389 298.3 0 357124 5265 10 381564 74.6 1 361732 19832 11 409069 18.6 1 379131 29938 12 445640 4.7 1 418576 27064 13 371519 1.2 1 343726 27793 14 407030 1.2 1 377761 29269 15 394357 1.2 1 367019 27338 16 424138 1.2 1 392651 31487 17 413729 1.2 1 385841 27888 18 382883 1.2 1 357587 25296 19 418080 1.2 1 391101 26979 20 417411 1.2 1 390369 27042 21 391108 1.2 1 362638 28470 22 408757 1.2 1 383321 25436 23 393814 1.2 1 369011 24803 24 412766 1.2 1 385708 27058 25 471235 1.2 1 444153 27082 26 350024 1.2 1 325902 24122 27 397639 1.2 1 369817 27822 28 384311 1.2 1 365334 18977 29 401600 1.2 1 378414 23186 30 395236 1.2 1 376122 19114 31 394822 1.2 1 373357 21465 32 385298 1.2 1 366431 18867 33 399697 1.2 1 374939 24758 34 415117 1.2 1 391453 23664 35 384868 1.2 1 363212 21656 36 659327 1.2 1 621294 38033 37 507203 1.2 1 483879 23324 38 304492 1.2 1 288746 15746 39 296264 1.2 1 281203 15061 40 470852 1.2 1 452591 18261 41 259522 1.2 1 244158 15364 42 572654 1.2 1 552085 20569 43 222572 1.2 1 206678 15894 44 625256 1.2 1 598412 26844 45 702038 1.2 1 674299 27739 46 494705 1.2 1 475948 18757 47 250853 1.2 1 240811 10042 48 147136 1.2 1 136438 10698 49 358439 1.2 1 344038 14401 50 249649 1.2 1 238344 11305 51 199048 1.2 1 188340 10708 52 303896 1.2 1 291832 12064 53 210722 1.2 1 198585 12137 54 457860 1.2 1 443475 14385 55 120848 1.2 1 111748 9100 56 305440 1.2 1 283518 21922 57 998481 1.2 1 970374 28107 58 180329 1.2 1 171158 9171 59 116785 1.2 1 106111 10674 60 524354 1.2 1 507313 17041 61 180736 1.2 1 170243 10493 62 327554 1.2 1 310625 16929 63 506382 1.2 1 487868 18514 64 446330 1.2 1 433304 13026 65 73949 1.2 1 69257 4692 66 109192 1.2 1 102378 6814 67 214512 1.2 1 206484 8028 68 149090 1.2 1 142909 6181 69 69425 1.2 1 64744 4681 70 153867 1.2 1 147938 5929 71 80198 1.2 1 75629 4569 72 101557 1.2 1 95775 5782 73 145609 1.2 1 138466 7143 74 155465 1.2 1 147923 7542 75 159520 1.2 1 152263 7257 76 116339 1.2 1 111346 4993 77 50516 1.2 1 47090 3426 78 95348 1.2 1 90287 5061 79 140311 1.2 1 133878 6433 80 148951 1.2 1 142454 6497 81 143448 1.2 1 136993 6455 82 135865 1.2 1 129452 6413 83 135967 1.2 1 129569 6398 84 128099 1.2 1 122316 5783 85 123123 1.2 1 117414 5709 86 113136 1.2 1 107634 5502 87 107555 1.2 1 102317 5238 88 101023 1.2 1 96209 4814 89 95718 1.2 1 91053 4665 90 91400 1.2 1 87034 4366 91 85664 1.2 1 81443 4221 92 80116 1.2 1 76135 3981 93 73885 1.2 1 70135 3750 94 69022 1.2 1 65595 3427 95 64635 1.2 1 61531 3104 96 61070 1.2 1 57912 3158 97 57154 1.2 1 54105 3049 98 53409 1.2 1 50430 2979 99 50276 1.2 1 47528 2748 100 46585 1.2 1 44041 2544 101 41923 1.2 1 39432 2491 102 37986 1.2 1 35777 2209 103 34666 1.2 1 32646 2020 104 32310 1.2 1 30269 2041 105 29339 1.2 1 27528 1811 106 27580 1.2 1 25824 1756 107 24918 1.2 1 23421 1497 108 22129 1.2 1 20628 1501 109 19519 1.2 1 18111 1408 110 17761 1.2 1 16342 1419 111 15873 1.2 1 14623 1250 112 14303 1.2 1 13142 1161 113 13031 1.2 1 11936 1095 114 12305 1.2 1 11225 1080 115 11537 1.2 1 10507 1030 116 10703 1.2 1 9682 1021 117 10337 1.2 1 9413 924 118 8557 1.2 1 7670 887 119 7393 1.2 1 6592 801 120 6751 1.2 1 6045 706 121 6160 1.2 1 5454 706 122 6048 1.2 1 5311 737 123 5430 1.2 1 4751 679 124 4891 1.2 1 4280 611 125 5107 1.2 1 4385 722 126 7783 1.2 1 6987 796 127 6776 1.2 1 6046 730 128 4498 1.2 1 3916 582 129 4199 1.2 1 3731 468 130 6765 1.2 1 6171 594 131 9581 1.2 1 8922 659 132 9830 1.2 1 9217 613 133 16128 1.2 1 15146 982 134 13224 1.2 1 12384 840 135 3563 1.2 1 3260 303 136 1575 1.2 1 1333 242 137 1108 1.2 1 907 201 138 789 1.2 1 636 153 139 599 1.2 1 462 137 140 476 1.2 1 365 111 141 398 1.2 1 317 81 142 243 1.2 1 158 85 143 175 1.2 1 133 42 144 193 1.2 1 161 32 145 483 1.2 1 438 45 146 386 1.2 1 340 46 147 2094 1.2 1 1904 190 148 1128 1.2 1 1025 103 149 449 1.2 1 404 45 150 4908 1.2 1 4708 200 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R2_001.fastq.gz ============================================= 78207503 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 78207503 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 535230 (0.68%)