SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_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/Meth7_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 2940.87 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 96,207,245 Reads with adapters: 65,385,386 (68.0%) Reads written (passing filters): 96,207,245 (100.0%) Total basepairs processed: 14,431,086,750 bp Quality-trimmed: 141,077,461 bp (1.0%) Total written (filtered): 12,438,890,323 bp (86.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 65385386 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 13.4% G: 20.1% T: 31.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18976422 24051811.2 0 18976422 2 2084710 6012952.8 0 2084710 3 1114269 1503238.2 0 1114269 4 725430 375809.6 0 725430 5 575667 93952.4 0 575667 6 479732 23488.1 0 479732 7 490148 5872.0 0 490148 8 553113 1468.0 0 553113 9 522583 367.0 0 515106 7477 10 526865 91.8 1 500542 26323 11 574255 22.9 1 532022 42233 12 618664 5.7 1 582766 35898 13 515306 1.4 1 477436 37870 14 567248 1.4 1 527150 40098 15 556525 1.4 1 517670 38855 16 600683 1.4 1 556105 44578 17 578663 1.4 1 539848 38815 18 551760 1.4 1 515289 36471 19 591009 1.4 1 552541 38468 20 614368 1.4 1 574530 39838 21 559014 1.4 1 518297 40717 22 590914 1.4 1 555307 35607 23 567898 1.4 1 532224 35674 24 602977 1.4 1 563732 39245 25 687263 1.4 1 647776 39487 26 511894 1.4 1 475420 36474 27 582949 1.4 1 540349 42600 28 566240 1.4 1 538534 27706 29 593508 1.4 1 558042 35466 30 585073 1.4 1 555540 29533 31 575808 1.4 1 543989 31819 32 578263 1.4 1 549329 28934 33 596984 1.4 1 560950 36034 34 620394 1.4 1 585134 35260 35 598011 1.4 1 552996 45015 36 2015543 1.4 1 1933590 81953 37 377082 1.4 1 353958 23124 38 347407 1.4 1 324143 23264 39 592172 1.4 1 565324 26848 40 453726 1.4 1 432610 21116 41 515119 1.4 1 487693 27426 42 638286 1.4 1 611756 26530 43 557445 1.4 1 526316 31129 44 839063 1.4 1 799731 39332 45 1205982 1.4 1 1158564 47418 46 532775 1.4 1 506220 26555 47 499256 1.4 1 482014 17242 48 162667 1.4 1 148284 14383 49 507253 1.4 1 485193 22060 50 346329 1.4 1 330530 15799 51 325411 1.4 1 307710 17701 52 434741 1.4 1 415955 18786 53 413056 1.4 1 391459 21597 54 756415 1.4 1 732185 24230 55 184485 1.4 1 169529 14956 56 514428 1.4 1 474010 40418 57 1816126 1.4 1 1765396 50730 58 293380 1.4 1 278459 14921 59 165112 1.4 1 146129 18983 60 974101 1.4 1 943492 30609 61 262487 1.4 1 248279 14208 62 339380 1.4 1 314753 24627 63 956017 1.4 1 919696 36321 64 966391 1.4 1 939647 26744 65 107259 1.4 1 99996 7263 66 175124 1.4 1 164258 10866 67 315204 1.4 1 303712 11492 68 190116 1.4 1 181736 8380 69 118894 1.4 1 111249 7645 70 224215 1.4 1 215523 8692 71 108384 1.4 1 102740 5644 72 119228 1.4 1 111869 7359 73 174139 1.4 1 165297 8842 74 183694 1.4 1 174810 8884 75 177881 1.4 1 168820 9061 76 164876 1.4 1 157771 7105 77 92427 1.4 1 86556 5871 78 176116 1.4 1 167530 8586 79 239174 1.4 1 228659 10515 80 256644 1.4 1 245471 11173 81 247199 1.4 1 236188 11011 82 234648 1.4 1 223875 10773 83 230736 1.4 1 220108 10628 84 220072 1.4 1 210112 9960 85 211986 1.4 1 202424 9562 86 195550 1.4 1 186387 9163 87 186259 1.4 1 177344 8915 88 176228 1.4 1 167985 8243 89 165856 1.4 1 157863 7993 90 159561 1.4 1 152195 7366 91 150635 1.4 1 143456 7179 92 141718 1.4 1 134942 6776 93 131393 1.4 1 125103 6290 94 122509 1.4 1 116488 6021 95 115329 1.4 1 109506 5823 96 108643 1.4 1 103045 5598 97 101748 1.4 1 96544 5204 98 94490 1.4 1 89763 4727 99 88228 1.4 1 83723 4505 100 83051 1.4 1 78528 4523 101 73833 1.4 1 69876 3957 102 66993 1.4 1 63319 3674 103 61193 1.4 1 57721 3472 104 56064 1.4 1 52809 3255 105 51256 1.4 1 48227 3029 106 46630 1.4 1 43636 2994 107 42299 1.4 1 39691 2608 108 37454 1.4 1 34998 2456 109 34020 1.4 1 31730 2290 110 29847 1.4 1 27644 2203 111 26771 1.4 1 24802 1969 112 23873 1.4 1 21997 1876 113 21652 1.4 1 19956 1696 114 18856 1.4 1 17302 1554 115 17153 1.4 1 15560 1593 116 15048 1.4 1 13714 1334 117 13387 1.4 1 12104 1283 118 12135 1.4 1 10704 1431 119 10592 1.4 1 9417 1175 120 8981 1.4 1 7894 1087 121 8107 1.4 1 6968 1139 122 7560 1.4 1 6604 956 123 6944 1.4 1 6036 908 124 6306 1.4 1 5395 911 125 6083 1.4 1 5205 878 126 7074 1.4 1 6206 868 127 6690 1.4 1 5839 851 128 4997 1.4 1 4326 671 129 4362 1.4 1 3742 620 130 4971 1.4 1 4334 637 131 5873 1.4 1 5304 569 132 5609 1.4 1 5003 606 133 8463 1.4 1 7578 885 134 6910 1.4 1 6215 695 135 2272 1.4 1 1910 362 136 1123 1.4 1 853 270 137 913 1.4 1 728 185 138 758 1.4 1 574 184 139 509 1.4 1 376 133 140 481 1.4 1 365 116 141 337 1.4 1 222 115 142 257 1.4 1 149 108 143 215 1.4 1 134 81 144 181 1.4 1 116 65 145 328 1.4 1 286 42 146 249 1.4 1 186 63 147 1151 1.4 1 1038 113 148 538 1.4 1 472 66 149 193 1.4 1 176 17 150 2436 1.4 1 2285 151 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R2_001.fastq.gz ============================================= 96207245 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 96207245 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 669920 (0.70%)