SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_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/Meth10_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 2698.65 s (32 us/read; 1.87 M reads/minute). === Summary === Total reads processed: 84,306,567 Reads with adapters: 53,624,774 (63.6%) Reads written (passing filters): 84,306,567 (100.0%) Total basepairs processed: 12,645,985,050 bp Quality-trimmed: 75,182,158 bp (0.6%) Total written (filtered): 11,165,536,073 bp (88.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 53624774 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.4% C: 13.8% G: 18.0% T: 31.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19861880 21076641.8 0 19861880 2 1919691 5269160.4 0 1919691 3 938882 1317290.1 0 938882 4 581539 329322.5 0 581539 5 417710 82330.6 0 417710 6 337488 20582.7 0 337488 7 350550 5145.7 0 350550 8 408184 1286.4 0 408184 9 361115 321.6 0 355523 5592 10 382240 80.4 1 362108 20132 11 403125 20.1 1 374482 28643 12 438645 5.0 1 412693 25952 13 366854 1.3 1 339064 27790 14 399359 1.3 1 370774 28585 15 389746 1.3 1 362683 27063 16 421360 1.3 1 390121 31239 17 407725 1.3 1 380115 27610 18 385026 1.3 1 360065 24961 19 412814 1.3 1 385972 26842 20 419745 1.3 1 392160 27585 21 402299 1.3 1 373621 28678 22 411642 1.3 1 386608 25034 23 395427 1.3 1 370768 24659 24 409110 1.3 1 383132 25978 25 460076 1.3 1 433219 26857 26 363609 1.3 1 339230 24379 27 410710 1.3 1 383749 26961 28 388904 1.3 1 370127 18777 29 411926 1.3 1 389192 22734 30 395973 1.3 1 377516 18457 31 402573 1.3 1 381565 21008 32 393127 1.3 1 375243 17884 33 405440 1.3 1 384543 20897 34 395339 1.3 1 377122 18217 35 403096 1.3 1 383058 20038 36 469682 1.3 1 450927 18755 37 319186 1.3 1 301015 18171 38 414422 1.3 1 395297 19125 39 374689 1.3 1 357579 17110 40 401797 1.3 1 381569 20228 41 422375 1.3 1 395747 26628 42 376856 1.3 1 360778 16078 43 380787 1.3 1 360831 19956 44 485085 1.3 1 463953 21132 45 480769 1.3 1 456655 24114 46 495436 1.3 1 472137 23299 47 475183 1.3 1 460530 14653 48 191099 1.3 1 179403 11696 49 337830 1.3 1 322459 15371 50 348754 1.3 1 335301 13453 51 268498 1.3 1 255291 13207 52 351429 1.3 1 336964 14465 53 320857 1.3 1 305649 15208 54 510701 1.3 1 494536 16165 55 165726 1.3 1 154976 10750 56 351621 1.3 1 329864 21757 57 964943 1.3 1 937820 27123 58 170614 1.3 1 160589 10025 59 194970 1.3 1 182061 12909 60 577410 1.3 1 559224 18186 61 247581 1.3 1 236520 11061 62 277529 1.3 1 255766 21763 63 997327 1.3 1 970448 26879 64 396317 1.3 1 384091 12226 65 106341 1.3 1 100330 6011 66 148416 1.3 1 138514 9902 67 379450 1.3 1 367444 12006 68 193454 1.3 1 185270 8184 69 149441 1.3 1 141806 7635 70 234751 1.3 1 226478 8273 71 132306 1.3 1 126216 6090 72 128359 1.3 1 121745 6614 73 172501 1.3 1 164901 7600 74 164649 1.3 1 157171 7478 75 156766 1.3 1 149699 7067 76 125797 1.3 1 120623 5174 77 85434 1.3 1 80328 5106 78 155992 1.3 1 149110 6882 79 185685 1.3 1 178073 7612 80 194628 1.3 1 186786 7842 81 182472 1.3 1 174825 7647 82 177081 1.3 1 169246 7835 83 178185 1.3 1 170505 7680 84 167040 1.3 1 160177 6863 85 162923 1.3 1 155900 7023 86 149004 1.3 1 142542 6462 87 143532 1.3 1 137166 6366 88 134654 1.3 1 128858 5796 89 127832 1.3 1 122136 5696 90 123410 1.3 1 118178 5232 91 116022 1.3 1 110763 5259 92 109152 1.3 1 104048 5104 93 101287 1.3 1 96394 4893 94 97356 1.3 1 92882 4474 95 93231 1.3 1 88963 4268 96 88567 1.3 1 84313 4254 97 82806 1.3 1 78748 4058 98 77404 1.3 1 73679 3725 99 72610 1.3 1 69005 3605 100 67605 1.3 1 64115 3490 101 63637 1.3 1 60508 3129 102 56294 1.3 1 53295 2999 103 51177 1.3 1 48278 2899 104 50081 1.3 1 47279 2802 105 47068 1.3 1 44438 2630 106 45671 1.3 1 42954 2717 107 42278 1.3 1 39869 2409 108 36017 1.3 1 33715 2302 109 31799 1.3 1 29732 2067 110 29269 1.3 1 27294 1975 111 25299 1.3 1 23500 1799 112 22399 1.3 1 20610 1789 113 21352 1.3 1 19574 1778 114 19410 1.3 1 17712 1698 115 19560 1.3 1 17907 1653 116 18865 1.3 1 17204 1661 117 19197 1.3 1 17411 1786 118 16286 1.3 1 14784 1502 119 13223 1.3 1 11975 1248 120 11471 1.3 1 10215 1256 121 10557 1.3 1 9300 1257 122 10138 1.3 1 9061 1077 123 10990 1.3 1 9826 1164 124 9554 1.3 1 8514 1040 125 10377 1.3 1 9259 1118 126 20897 1.3 1 18962 1935 127 18296 1.3 1 16420 1876 128 9271 1.3 1 8180 1091 129 9240 1.3 1 8246 994 130 19574 1.3 1 17688 1886 131 37197 1.3 1 34730 2467 132 40733 1.3 1 38389 2344 133 67102 1.3 1 62904 4198 134 58466 1.3 1 54589 3877 135 17538 1.3 1 16342 1196 136 4875 1.3 1 4393 482 137 3204 1.3 1 2733 471 138 2278 1.3 1 1888 390 139 898 1.3 1 679 219 140 830 1.3 1 675 155 141 400 1.3 1 267 133 142 275 1.3 1 163 112 143 244 1.3 1 147 97 144 414 1.3 1 326 88 145 1650 1.3 1 1513 137 146 1285 1.3 1 1092 193 147 7354 1.3 1 6274 1080 148 4475 1.3 1 3775 700 149 1545 1.3 1 1335 210 150 16219 1.3 1 15040 1179 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R2_001.fastq.gz ============================================= 84306567 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 84306567 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 923660 (1.10%)