SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_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/Meth9_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 2657.61 s (30 us/read; 1.98 M reads/minute). === Summary === Total reads processed: 87,891,647 Reads with adapters: 60,091,932 (68.4%) Reads written (passing filters): 87,891,647 (100.0%) Total basepairs processed: 13,183,747,050 bp Quality-trimmed: 102,987,221 bp (0.8%) Total written (filtered): 11,269,063,168 bp (85.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60091932 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 14.0% G: 20.8% T: 31.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16863866 21972911.8 0 16863866 2 1852658 5493227.9 0 1852658 3 977867 1373307.0 0 977867 4 639712 343326.7 0 639712 5 514286 85831.7 0 514286 6 425910 21457.9 0 425910 7 440303 5364.5 0 440303 8 531132 1341.1 0 531132 9 421023 335.3 0 414358 6665 10 473612 83.8 1 443457 30155 11 503048 21.0 1 463047 40001 12 538489 5.2 1 499991 38498 13 477709 1.3 1 436900 40809 14 514614 1.3 1 472741 41873 15 499528 1.3 1 462169 37359 16 533681 1.3 1 490320 43361 17 536141 1.3 1 495121 41020 18 477513 1.3 1 443644 33869 19 540324 1.3 1 501090 39234 20 540333 1.3 1 501060 39273 21 499777 1.3 1 461229 38548 22 529211 1.3 1 493145 36066 23 513863 1.3 1 478576 35287 24 548989 1.3 1 508901 40088 25 618339 1.3 1 579119 39220 26 472131 1.3 1 438173 33958 27 510995 1.3 1 474482 36513 28 516235 1.3 1 489118 27117 29 531926 1.3 1 501713 30213 30 537338 1.3 1 509401 27937 31 514166 1.3 1 486556 27610 32 549655 1.3 1 521505 28150 33 535265 1.3 1 506879 28386 34 516983 1.3 1 488239 28744 35 529970 1.3 1 503823 26147 36 525560 1.3 1 497685 27875 37 555810 1.3 1 527476 28334 38 539527 1.3 1 511066 28461 39 504000 1.3 1 475682 28318 40 510954 1.3 1 486703 24251 41 513428 1.3 1 486306 27122 42 642433 1.3 1 608269 34164 43 449405 1.3 1 422113 27292 44 887164 1.3 1 845889 41275 45 706281 1.3 1 671104 35177 46 456874 1.3 1 429976 26898 47 804981 1.3 1 778258 26723 48 164303 1.3 1 152308 11995 49 411518 1.3 1 391507 20011 50 426878 1.3 1 409568 17310 51 309958 1.3 1 293861 16097 52 418002 1.3 1 398925 19077 53 458565 1.3 1 434668 23897 54 757643 1.3 1 730811 26832 55 192405 1.3 1 178438 13967 56 493727 1.3 1 458732 34995 57 1620116 1.3 1 1569153 50963 58 235380 1.3 1 220684 14696 59 215900 1.3 1 197773 18127 60 897185 1.3 1 865130 32055 61 273893 1.3 1 260569 13324 62 306206 1.3 1 279460 26746 63 1283571 1.3 1 1240821 42750 64 798128 1.3 1 771242 26886 65 118897 1.3 1 111299 7598 66 192185 1.3 1 179490 12695 67 423318 1.3 1 408525 14793 68 211686 1.3 1 201863 9823 69 183174 1.3 1 173135 10039 70 291566 1.3 1 280726 10840 71 141818 1.3 1 134980 6838 72 139518 1.3 1 131687 7831 73 191727 1.3 1 183017 8710 74 186722 1.3 1 178387 8335 75 160604 1.3 1 152691 7913 76 142460 1.3 1 135492 6968 77 147016 1.3 1 139131 7885 78 231621 1.3 1 221287 10334 79 260377 1.3 1 248742 11635 80 275092 1.3 1 263128 11964 81 252094 1.3 1 240762 11332 82 235967 1.3 1 225042 10925 83 232988 1.3 1 221903 11085 84 223995 1.3 1 213699 10296 85 210974 1.3 1 201328 9646 86 199512 1.3 1 190102 9410 87 189886 1.3 1 180736 9150 88 177954 1.3 1 169537 8417 89 169290 1.3 1 161278 8012 90 166003 1.3 1 158270 7733 91 152653 1.3 1 145358 7295 92 142895 1.3 1 135742 7153 93 135571 1.3 1 128727 6844 94 127887 1.3 1 121344 6543 95 122022 1.3 1 115812 6210 96 115619 1.3 1 109893 5726 97 107721 1.3 1 102250 5471 98 101041 1.3 1 95920 5121 99 93942 1.3 1 89108 4834 100 87563 1.3 1 82808 4755 101 79137 1.3 1 74821 4316 102 72144 1.3 1 68020 4124 103 65976 1.3 1 62262 3714 104 60961 1.3 1 57381 3580 105 56651 1.3 1 53309 3342 106 52401 1.3 1 49030 3371 107 47820 1.3 1 44780 3040 108 42625 1.3 1 39713 2912 109 38430 1.3 1 35835 2595 110 34910 1.3 1 32479 2431 111 31398 1.3 1 29062 2336 112 28817 1.3 1 26615 2202 113 25795 1.3 1 23692 2103 114 24181 1.3 1 22109 2072 115 22343 1.3 1 20459 1884 116 21556 1.3 1 19696 1860 117 20108 1.3 1 18334 1774 118 17683 1.3 1 15918 1765 119 14350 1.3 1 12875 1475 120 13126 1.3 1 11696 1430 121 11540 1.3 1 10344 1196 122 11128 1.3 1 9768 1360 123 10509 1.3 1 9247 1262 124 9408 1.3 1 8162 1246 125 9376 1.3 1 8148 1228 126 11877 1.3 1 10640 1237 127 10540 1.3 1 9382 1158 128 8027 1.3 1 7055 972 129 8292 1.3 1 7260 1032 130 10884 1.3 1 9769 1115 131 15854 1.3 1 14666 1188 132 14466 1.3 1 13377 1089 133 21448 1.3 1 19943 1505 134 17180 1.3 1 15932 1248 135 4967 1.3 1 4407 560 136 2064 1.3 1 1692 372 137 1436 1.3 1 1144 292 138 1215 1.3 1 910 305 139 895 1.3 1 649 246 140 807 1.3 1 630 177 141 516 1.3 1 367 149 142 363 1.3 1 241 122 143 296 1.3 1 175 121 144 188 1.3 1 141 47 145 341 1.3 1 290 51 146 373 1.3 1 300 73 147 2047 1.3 1 1820 227 148 1227 1.3 1 1069 158 149 331 1.3 1 275 56 150 4180 1.3 1 3958 222 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R2_001.fastq.gz ============================================= 87891647 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 87891647 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 857936 (0.98%)