SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_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/Meth8_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 2608.31 s (30 us/read; 1.98 M reads/minute). === Summary === Total reads processed: 86,019,978 Reads with adapters: 58,906,572 (68.5%) Reads written (passing filters): 86,019,978 (100.0%) Total basepairs processed: 12,902,996,700 bp Quality-trimmed: 72,570,856 bp (0.6%) Total written (filtered): 11,013,524,647 bp (85.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58906572 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.0% C: 17.3% G: 16.8% T: 30.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16528924 21504994.5 0 16528924 2 1852713 5376248.6 0 1852713 3 902077 1344062.2 0 902077 4 603529 336015.5 0 603529 5 468971 84003.9 0 468971 6 408734 21001.0 0 408734 7 429921 5250.2 0 429921 8 464410 1312.6 0 464410 9 429657 328.1 0 419930 9727 10 455273 82.0 1 427521 27752 11 474161 20.5 1 440146 34015 12 481402 5.1 1 450977 30425 13 467127 1.3 1 435837 31290 14 483123 1.3 1 448049 35074 15 479400 1.3 1 446160 33240 16 486536 1.3 1 450447 36089 17 504765 1.3 1 467752 37013 18 483633 1.3 1 452185 31448 19 480864 1.3 1 448016 32848 20 489046 1.3 1 456461 32585 21 498117 1.3 1 464266 33851 22 490208 1.3 1 457667 32541 23 504406 1.3 1 469231 35175 24 499630 1.3 1 461451 38179 25 498584 1.3 1 465317 33267 26 491535 1.3 1 459758 31777 27 507136 1.3 1 474063 33073 28 492573 1.3 1 461740 30833 29 497576 1.3 1 465602 31974 30 493742 1.3 1 466072 27670 31 489033 1.3 1 460652 28381 32 498868 1.3 1 471076 27792 33 490983 1.3 1 461542 29441 34 503013 1.3 1 472964 30049 35 491984 1.3 1 463819 28165 36 495957 1.3 1 468056 27901 37 493873 1.3 1 465789 28084 38 497920 1.3 1 467409 30511 39 496904 1.3 1 467419 29485 40 507826 1.3 1 479097 28729 41 483843 1.3 1 455669 28174 42 538087 1.3 1 507648 30439 43 479845 1.3 1 440795 39050 44 505837 1.3 1 469329 36508 45 687694 1.3 1 654361 33333 46 316234 1.3 1 291496 24738 47 581107 1.3 1 487049 94058 48 3294957 1.3 1 3168271 126686 49 594387 1.3 1 565016 29371 50 247543 1.3 1 214064 33479 51 1136150 1.3 1 1089965 46185 52 356228 1.3 1 339424 16804 53 122866 1.3 1 104004 18862 54 677671 1.3 1 645294 32377 55 493584 1.3 1 474002 19582 56 163879 1.3 1 153295 10584 57 240847 1.3 1 231045 9802 58 120478 1.3 1 107622 12856 59 416596 1.3 1 401656 14940 60 83853 1.3 1 78143 5710 61 126254 1.3 1 114871 11383 62 339648 1.3 1 325408 14240 63 158472 1.3 1 151491 6981 64 112244 1.3 1 103689 8555 65 339639 1.3 1 323770 15869 66 322079 1.3 1 309328 12751 67 103591 1.3 1 94260 9331 68 291022 1.3 1 274365 16657 69 337994 1.3 1 311452 26542 70 632946 1.3 1 603667 29279 71 316247 1.3 1 301938 14309 72 117180 1.3 1 110904 6276 73 42755 1.3 1 37435 5320 74 146711 1.3 1 135823 10888 75 255699 1.3 1 239816 15883 76 297589 1.3 1 280478 17111 77 287906 1.3 1 270462 17444 78 289192 1.3 1 271745 17447 79 286225 1.3 1 269110 17115 80 274745 1.3 1 258074 16671 81 267028 1.3 1 250429 16599 82 267287 1.3 1 251466 15821 83 254363 1.3 1 238757 15606 84 242273 1.3 1 227034 15239 85 240149 1.3 1 225429 14720 86 232423 1.3 1 218170 14253 87 229302 1.3 1 215535 13767 88 212996 1.3 1 199905 13091 89 193416 1.3 1 180844 12572 90 183933 1.3 1 171557 12376 91 178230 1.3 1 166332 11898 92 172236 1.3 1 160982 11254 93 164837 1.3 1 153859 10978 94 157453 1.3 1 146982 10471 95 147480 1.3 1 137660 9820 96 139337 1.3 1 129883 9454 97 132238 1.3 1 123217 9021 98 123215 1.3 1 114629 8586 99 114660 1.3 1 106699 7961 100 107074 1.3 1 99402 7672 101 99938 1.3 1 92696 7242 102 92431 1.3 1 85529 6902 103 86595 1.3 1 80059 6536 104 79827 1.3 1 73546 6281 105 73802 1.3 1 67892 5910 106 68924 1.3 1 63381 5543 107 61984 1.3 1 56946 5038 108 56820 1.3 1 52008 4812 109 51537 1.3 1 46930 4607 110 46426 1.3 1 42196 4230 111 42265 1.3 1 38340 3925 112 38430 1.3 1 34744 3686 113 35302 1.3 1 31711 3591 114 31474 1.3 1 28195 3279 115 28532 1.3 1 25602 2930 116 25617 1.3 1 22983 2634 117 23248 1.3 1 20662 2586 118 20564 1.3 1 18229 2335 119 18261 1.3 1 16029 2232 120 16410 1.3 1 14423 1987 121 14549 1.3 1 12577 1972 122 13654 1.3 1 11892 1762 123 13135 1.3 1 11303 1832 124 11428 1.3 1 9780 1648 125 11031 1.3 1 9440 1591 126 13859 1.3 1 12104 1755 127 12255 1.3 1 10790 1465 128 8719 1.3 1 7528 1191 129 8525 1.3 1 7544 981 130 9508 1.3 1 8385 1123 131 14036 1.3 1 12924 1112 132 13809 1.3 1 12664 1145 133 18443 1.3 1 17138 1305 134 16329 1.3 1 15153 1176 135 4723 1.3 1 4181 542 136 2040 1.3 1 1646 394 137 1375 1.3 1 1036 339 138 1127 1.3 1 848 279 139 650 1.3 1 480 170 140 555 1.3 1 365 190 141 346 1.3 1 202 144 142 282 1.3 1 159 123 143 241 1.3 1 130 111 144 198 1.3 1 132 66 145 439 1.3 1 367 72 146 865 1.3 1 776 89 147 6317 1.3 1 5747 570 148 3369 1.3 1 3017 352 149 787 1.3 1 712 75 150 11703 1.3 1 10957 746 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R1_001.fastq.gz ============================================= 86019978 sequences processed in total