SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_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/Meth10_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 2619.14 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 84,306,567 Reads with adapters: 54,788,380 (65.0%) Reads written (passing filters): 84,306,567 (100.0%) Total basepairs processed: 12,645,985,050 bp Quality-trimmed: 16,741,512 bp (0.1%) Total written (filtered): 11,144,101,263 bp (88.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 54788380 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.3% C: 16.9% G: 14.5% T: 30.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20087171 21076641.8 0 20087171 2 1813918 5269160.4 0 1813918 3 873915 1317290.1 0 873915 4 558229 329322.5 0 558229 5 415119 82330.6 0 415119 6 349731 20582.7 0 349731 7 372849 5145.7 0 372849 8 408592 1286.4 0 408592 9 374071 321.6 0 365399 8672 10 397601 80.4 1 373645 23956 11 412375 20.1 1 383235 29140 12 417766 5.0 1 391425 26341 13 401873 1.3 1 374959 26914 14 413498 1.3 1 383743 29755 15 410252 1.3 1 381745 28507 16 418895 1.3 1 388384 30511 17 433797 1.3 1 402985 30812 18 411876 1.3 1 385337 26539 19 405157 1.3 1 378241 26916 20 417320 1.3 1 389068 28252 21 425512 1.3 1 396360 29152 22 414020 1.3 1 386540 27480 23 426843 1.3 1 397519 29324 24 419542 1.3 1 388690 30852 25 419316 1.3 1 391778 27538 26 414854 1.3 1 387552 27302 27 426656 1.3 1 398584 28072 28 410941 1.3 1 385217 25724 29 418300 1.3 1 391761 26539 30 412229 1.3 1 388918 23311 31 406287 1.3 1 382845 23442 32 410526 1.3 1 387548 22978 33 409786 1.3 1 384961 24825 34 425411 1.3 1 400165 25246 35 398975 1.3 1 377322 21653 36 408651 1.3 1 384528 24123 37 410983 1.3 1 386751 24232 38 406065 1.3 1 382456 23609 39 403998 1.3 1 381336 22662 40 397942 1.3 1 375225 22717 41 434330 1.3 1 409437 24893 42 383620 1.3 1 360445 23175 43 397784 1.3 1 369631 28153 44 396544 1.3 1 370154 26390 45 522637 1.3 1 498900 23737 46 253725 1.3 1 236592 17133 47 381386 1.3 1 359409 21977 48 397939 1.3 1 375666 22273 49 377989 1.3 1 356497 21492 50 369415 1.3 1 346468 22947 51 405549 1.3 1 381238 24311 52 355894 1.3 1 336154 19740 53 350710 1.3 1 330270 20440 54 369432 1.3 1 347007 22425 55 370880 1.3 1 350472 20408 56 344709 1.3 1 324826 19883 57 358913 1.3 1 338694 20219 58 366734 1.3 1 346501 20233 59 335781 1.3 1 316350 19431 60 329821 1.3 1 312040 17781 61 307437 1.3 1 289200 18237 62 337215 1.3 1 317800 19415 63 339253 1.3 1 320983 18270 64 307533 1.3 1 290898 16635 65 284690 1.3 1 267115 17575 66 330662 1.3 1 311833 18829 67 324655 1.3 1 305761 18894 68 346463 1.3 1 326661 19802 69 343819 1.3 1 315151 28668 70 687320 1.3 1 661746 25574 71 75523 1.3 1 70809 4714 72 42649 1.3 1 37975 4674 73 120214 1.3 1 111212 9002 74 209861 1.3 1 197410 12451 75 233269 1.3 1 220078 13191 76 232990 1.3 1 219691 13299 77 227410 1.3 1 213929 13481 78 221915 1.3 1 208486 13429 79 215689 1.3 1 202835 12854 80 207250 1.3 1 194747 12503 81 201334 1.3 1 189702 11632 82 196748 1.3 1 184523 12225 83 190989 1.3 1 179763 11226 84 179219 1.3 1 168329 10890 85 175756 1.3 1 164936 10820 86 168289 1.3 1 158051 10238 87 167282 1.3 1 157274 10008 88 144104 1.3 1 134747 9357 89 135448 1.3 1 126378 9070 90 131499 1.3 1 122793 8706 91 127264 1.3 1 118736 8528 92 121114 1.3 1 113141 7973 93 113184 1.3 1 105860 7324 94 110374 1.3 1 102866 7508 95 104676 1.3 1 97419 7257 96 98069 1.3 1 91264 6805 97 91188 1.3 1 84762 6426 98 84155 1.3 1 78003 6152 99 78241 1.3 1 72477 5764 100 72641 1.3 1 67136 5505 101 69950 1.3 1 64581 5369 102 62894 1.3 1 58044 4850 103 57552 1.3 1 52942 4610 104 56649 1.3 1 51800 4849 105 52762 1.3 1 48230 4532 106 50188 1.3 1 45983 4205 107 47175 1.3 1 42914 4261 108 40194 1.3 1 36615 3579 109 34610 1.3 1 31470 3140 110 32291 1.3 1 29173 3118 111 28366 1.3 1 25552 2814 112 25385 1.3 1 22723 2662 113 23983 1.3 1 21292 2691 114 21024 1.3 1 18758 2266 115 20728 1.3 1 18438 2290 116 18385 1.3 1 16280 2105 117 18416 1.3 1 16258 2158 118 16190 1.3 1 14284 1906 119 13662 1.3 1 11866 1796 120 11982 1.3 1 10483 1499 121 10731 1.3 1 9124 1607 122 10985 1.3 1 9479 1506 123 12829 1.3 1 11132 1697 124 10226 1.3 1 8902 1324 125 11092 1.3 1 9647 1445 126 23421 1.3 1 20930 2491 127 20964 1.3 1 18444 2520 128 10521 1.3 1 9003 1518 129 9578 1.3 1 8324 1254 130 16881 1.3 1 15062 1819 131 35161 1.3 1 32891 2270 132 41035 1.3 1 38490 2545 133 59794 1.3 1 55833 3961 134 57318 1.3 1 53691 3627 135 18130 1.3 1 16692 1438 136 4809 1.3 1 4181 628 137 3107 1.3 1 2644 463 138 2705 1.3 1 2179 526 139 1017 1.3 1 724 293 140 980 1.3 1 691 289 141 368 1.3 1 214 154 142 237 1.3 1 143 94 143 211 1.3 1 121 90 144 476 1.3 1 337 139 145 1579 1.3 1 1325 254 146 2140 1.3 1 1799 341 147 16319 1.3 1 14071 2248 148 10062 1.3 1 8487 1575 149 2880 1.3 1 2480 400 150 38413 1.3 1 34718 3695 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R1_001.fastq.gz ============================================= 84306567 sequences processed in total