SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_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/Meth3_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 2458.49 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 78,207,503 Reads with adapters: 50,905,854 (65.1%) Reads written (passing filters): 78,207,503 (100.0%) Total basepairs processed: 11,731,125,450 bp Quality-trimmed: 14,629,344 bp (0.1%) Total written (filtered): 10,447,177,853 bp (89.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 50905854 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.8% C: 15.8% G: 14.6% T: 30.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18817186 19551875.8 0 18817186 2 1783364 4887968.9 0 1783364 3 892389 1221992.2 0 892389 4 569400 305498.1 0 569400 5 423376 76374.5 0 423376 6 353954 19093.6 0 353954 7 376976 4773.4 0 376976 8 404842 1193.4 0 404842 9 383998 298.3 0 374161 9837 10 398945 74.6 1 372433 26512 11 419208 18.6 1 386656 32552 12 428299 4.7 1 398529 29770 13 408665 1.2 1 378326 30339 14 420407 1.2 1 387104 33303 15 415779 1.2 1 384698 31081 16 425713 1.2 1 391243 34470 17 440543 1.2 1 405444 35099 18 417127 1.2 1 386514 30613 19 417440 1.2 1 381450 35990 20 592704 1.2 1 559369 33335 21 231658 1.2 1 208654 23004 22 415710 1.2 1 385594 30116 23 421739 1.2 1 389550 32189 24 420590 1.2 1 386019 34571 25 417350 1.2 1 386691 30659 26 413517 1.2 1 382950 30567 27 425625 1.2 1 394344 31281 28 409930 1.2 1 381716 28214 29 408321 1.2 1 378347 29974 30 409954 1.2 1 383875 26079 31 401045 1.2 1 374303 26742 32 402276 1.2 1 375995 26281 33 402045 1.2 1 373824 28221 34 414761 1.2 1 386170 28591 35 393735 1.2 1 367518 26217 36 399759 1.2 1 373763 25996 37 401927 1.2 1 374767 27160 38 388944 1.2 1 362977 25967 39 391373 1.2 1 365701 25672 40 381102 1.2 1 354682 26420 41 387443 1.2 1 361149 26294 42 381731 1.2 1 354861 26870 43 407676 1.2 1 380344 27332 44 357090 1.2 1 327702 29388 45 520315 1.2 1 494123 26192 46 210639 1.2 1 192990 17649 47 353811 1.2 1 330336 23475 48 376826 1.2 1 352451 24375 49 349095 1.2 1 326037 23058 50 342832 1.2 1 318729 24103 51 363752 1.2 1 338574 25178 52 332956 1.2 1 311367 21589 53 326829 1.2 1 305003 21826 54 337460 1.2 1 313355 24105 55 339870 1.2 1 317368 22502 56 311904 1.2 1 291006 20898 57 323083 1.2 1 301244 21839 58 324642 1.2 1 303248 21394 59 305142 1.2 1 283969 21173 60 297671 1.2 1 278735 18936 61 276080 1.2 1 256957 19123 62 299046 1.2 1 278885 20161 63 295827 1.2 1 276987 18840 64 272339 1.2 1 255033 17306 65 245991 1.2 1 227775 18216 66 288339 1.2 1 268412 19927 67 287848 1.2 1 267360 20488 68 299672 1.2 1 278833 20839 69 295519 1.2 1 266251 29268 70 570524 1.2 1 545560 24964 71 57451 1.2 1 53306 4145 72 35309 1.2 1 30622 4687 73 106668 1.2 1 97282 9386 74 176529 1.2 1 163971 12558 75 193880 1.2 1 180697 13183 76 190907 1.2 1 177555 13352 77 185648 1.2 1 172591 13057 78 178529 1.2 1 165843 12686 79 173796 1.2 1 161433 12363 80 166512 1.2 1 154297 12215 81 158669 1.2 1 147242 11427 82 152136 1.2 1 140959 11177 83 148455 1.2 1 137752 10703 84 140525 1.2 1 130109 10416 85 135307 1.2 1 125401 9906 86 129878 1.2 1 120437 9441 87 127114 1.2 1 118137 8977 88 109146 1.2 1 100293 8853 89 102693 1.2 1 94474 8219 90 99179 1.2 1 91224 7955 91 94918 1.2 1 87265 7653 92 89739 1.2 1 82767 6972 93 84019 1.2 1 77306 6713 94 80177 1.2 1 73547 6630 95 73687 1.2 1 67531 6156 96 69046 1.2 1 63301 5745 97 64353 1.2 1 58824 5529 98 59004 1.2 1 53973 5031 99 55232 1.2 1 50308 4924 100 51146 1.2 1 46429 4717 101 46745 1.2 1 42408 4337 102 43477 1.2 1 39414 4063 103 40009 1.2 1 36090 3919 104 37133 1.2 1 33555 3578 105 33471 1.2 1 29999 3472 106 31753 1.2 1 28541 3212 107 28501 1.2 1 25396 3105 108 25705 1.2 1 22845 2860 109 22666 1.2 1 20018 2648 110 20438 1.2 1 18101 2337 111 18683 1.2 1 16379 2304 112 16807 1.2 1 14757 2050 113 15324 1.2 1 13182 2142 114 14175 1.2 1 12324 1851 115 13144 1.2 1 11369 1775 116 11693 1.2 1 10123 1570 117 10822 1.2 1 9357 1465 118 9339 1.2 1 7947 1392 119 8393 1.2 1 7216 1177 120 7446 1.2 1 6375 1071 121 6919 1.2 1 5850 1069 122 6889 1.2 1 5796 1093 123 6093 1.2 1 5076 1017 124 5367 1.2 1 4593 774 125 5326 1.2 1 4452 874 126 8640 1.2 1 7514 1126 127 7616 1.2 1 6486 1130 128 5120 1.2 1 4334 786 129 4442 1.2 1 3874 568 130 6057 1.2 1 5296 761 131 8942 1.2 1 8185 757 132 9735 1.2 1 8905 830 133 14509 1.2 1 13462 1047 134 13139 1.2 1 12133 1006 135 3664 1.2 1 3222 442 136 1502 1.2 1 1202 300 137 976 1.2 1 770 206 138 828 1.2 1 590 238 139 536 1.2 1 374 162 140 515 1.2 1 348 167 141 311 1.2 1 196 115 142 248 1.2 1 135 113 143 160 1.2 1 86 74 144 179 1.2 1 130 49 145 442 1.2 1 392 50 146 544 1.2 1 463 81 147 4447 1.2 1 3941 506 148 2391 1.2 1 2095 296 149 1013 1.2 1 902 111 150 10300 1.2 1 9636 664 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R1_001.fastq.gz ============================================= 78207503 sequences processed in total