SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L002_R2_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 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 before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 3884.21 s (48 us/read; 1.26 M reads/minute). === Summary === Total reads processed: 81,699,034 Reads with adapters: 57,979,113 (71.0%) Reads written (passing filters): 81,699,034 (100.0%) Total basepairs processed: 12,254,855,100 bp Quality-trimmed: 41,067,962 bp (0.3%) Total written (filtered): 10,294,963,583 bp (84.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57979113 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.7% C: 9.9% G: 22.0% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15214651 20424758.5 0 15214651 2 1629144 5106189.6 0 1629144 3 914799 1276547.4 0 914799 4 558975 319136.9 0 558975 5 482109 79784.2 0 482109 6 418136 19946.1 0 418136 7 337570 4986.5 0 337570 8 479586 1246.6 0 479586 9 390650 311.7 0 389615 1035 10 405041 77.9 1 379605 25436 11 435020 19.5 1 401922 33098 12 439217 4.9 1 406727 32490 13 510754 1.2 1 472376 38378 14 448612 1.2 1 412140 36472 15 384027 1.2 1 355388 28639 16 544298 1.2 1 502865 41433 17 437427 1.2 1 403719 33708 18 402979 1.2 1 373023 29956 19 503067 1.2 1 466488 36579 20 474971 1.2 1 440326 34645 21 421874 1.2 1 390910 30964 22 467522 1.2 1 433687 33835 23 490952 1.2 1 454530 36422 24 482710 1.2 1 447678 35032 25 536922 1.2 1 501311 35611 26 451785 1.2 1 415820 35965 27 506974 1.2 1 466123 40851 28 440254 1.2 1 412940 27314 29 498335 1.2 1 462544 35791 30 447616 1.2 1 418293 29323 31 531574 1.2 1 494290 37284 32 441801 1.2 1 413285 28516 33 515665 1.2 1 478090 37575 34 666212 1.2 1 619804 46408 35 346551 1.2 1 323116 23435 36 489499 1.2 1 454133 35366 37 532182 1.2 1 495525 36657 38 478707 1.2 1 449260 29447 39 471359 1.2 1 443454 27905 40 529670 1.2 1 494697 34973 41 516177 1.2 1 483272 32905 42 520597 1.2 1 487926 32671 43 474470 1.2 1 444318 30152 44 553215 1.2 1 517017 36198 45 566191 1.2 1 530084 36107 46 413041 1.2 1 386808 26233 47 502147 1.2 1 473043 29104 48 484308 1.2 1 456231 28077 49 510392 1.2 1 478462 31930 50 506166 1.2 1 473768 32398 51 605207 1.2 1 567914 37293 52 440187 1.2 1 413511 26676 53 531819 1.2 1 501544 30275 54 389426 1.2 1 367011 22415 55 491938 1.2 1 464562 27376 56 495033 1.2 1 464600 30433 57 481452 1.2 1 455340 26112 58 468033 1.2 1 442245 25788 59 468551 1.2 1 441634 26917 60 478522 1.2 1 450900 27622 61 487423 1.2 1 460617 26806 62 522057 1.2 1 491364 30693 63 673446 1.2 1 638844 34602 64 507915 1.2 1 484583 23332 65 350472 1.2 1 331804 18668 66 389451 1.2 1 368357 21094 67 396849 1.2 1 374262 22587 68 394541 1.2 1 372684 21857 69 391045 1.2 1 368794 22251 70 390887 1.2 1 368825 22062 71 401886 1.2 1 379624 22262 72 392080 1.2 1 370490 21590 73 411065 1.2 1 388688 22377 74 374532 1.2 1 353760 20772 75 357961 1.2 1 338145 19816 76 346375 1.2 1 327002 19373 77 331945 1.2 1 313179 18766 78 321538 1.2 1 303798 17740 79 313177 1.2 1 295979 17198 80 304441 1.2 1 287925 16516 81 293724 1.2 1 277950 15774 82 282766 1.2 1 267333 15433 83 270058 1.2 1 255507 14551 84 265196 1.2 1 251091 14105 85 257861 1.2 1 244467 13394 86 250545 1.2 1 237466 13079 87 251526 1.2 1 238890 12636 88 240557 1.2 1 228280 12277 89 211890 1.2 1 200619 11271 90 199074 1.2 1 188762 10312 91 188118 1.2 1 178454 9664 92 176434 1.2 1 167450 8984 93 173462 1.2 1 164594 8868 94 163597 1.2 1 155286 8311 95 151070 1.2 1 143169 7901 96 142096 1.2 1 134776 7320 97 132469 1.2 1 125885 6584 98 123111 1.2 1 116966 6145 99 116382 1.2 1 110385 5997 100 108683 1.2 1 103116 5567 101 96750 1.2 1 91809 4941 102 88826 1.2 1 84306 4520 103 81399 1.2 1 77208 4191 104 76198 1.2 1 72290 3908 105 68158 1.2 1 64724 3434 106 61130 1.2 1 58100 3030 107 52011 1.2 1 49328 2683 108 45529 1.2 1 43239 2290 109 41683 1.2 1 39576 2107 110 36218 1.2 1 34303 1915 111 32883 1.2 1 31247 1636 112 29793 1.2 1 28318 1475 113 24999 1.2 1 23719 1280 114 22662 1.2 1 21525 1137 115 18096 1.2 1 17176 920 116 15270 1.2 1 14496 774 117 12170 1.2 1 11514 656 118 10414 1.2 1 9832 582 119 8403 1.2 1 7959 444 120 7343 1.2 1 6952 391 121 6317 1.2 1 5964 353 122 5204 1.2 1 4941 263 123 4340 1.2 1 4122 218 124 3564 1.2 1 3376 188 125 2965 1.2 1 2783 182 126 2377 1.2 1 2237 140 127 1922 1.2 1 1812 110 128 1530 1.2 1 1436 94 129 1224 1.2 1 1157 67 130 1037 1.2 1 967 70 131 861 1.2 1 806 55 132 686 1.2 1 633 53 133 661 1.2 1 620 41 134 651 1.2 1 603 48 135 432 1.2 1 408 24 136 309 1.2 1 286 23 137 192 1.2 1 170 22 138 168 1.2 1 155 13 139 128 1.2 1 109 19 140 85 1.2 1 78 7 141 53 1.2 1 46 7 142 58 1.2 1 51 7 143 31 1.2 1 26 5 144 40 1.2 1 32 8 145 40 1.2 1 33 7 146 40 1.2 1 29 11 147 75 1.2 1 67 8 148 58 1.2 1 52 6 149 37 1.2 1 34 3 150 319 1.2 1 294 25 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L002_R2_001.fastq.gz ============================================= 81699034 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 70001 (0.1%)