SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L002_R1_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_F1_S20_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 5100.56 s (45 us/read; 1.33 M reads/minute). === Summary === Total reads processed: 112,706,276 Reads with adapters: 78,369,527 (69.5%) Reads written (passing filters): 112,706,276 (100.0%) Total basepairs processed: 16,905,941,400 bp Quality-trimmed: 25,158,265 bp (0.1%) Total written (filtered): 14,312,572,664 bp (84.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 78369527 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.1% C: 9.8% G: 19.7% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22613071 28176569.0 0 22613071 2 2300394 7044142.2 0 2300394 3 1191481 1761035.6 0 1191481 4 736265 440258.9 0 736265 5 556744 110064.7 0 556744 6 521852 27516.2 0 521852 7 432500 6879.0 0 432500 8 542896 1719.8 0 542896 9 541192 429.9 0 533921 7271 10 495976 107.5 1 461928 34048 11 558120 26.9 1 506660 51460 12 551298 6.7 1 505922 45376 13 542939 1.7 1 497854 45085 14 564136 1.7 1 512614 51522 15 569498 1.7 1 521423 48075 16 563578 1.7 1 509820 53758 17 682231 1.7 1 615144 67087 18 558002 1.7 1 512187 45815 19 496544 1.7 1 454420 42124 20 576298 1.7 1 529271 47027 21 637299 1.7 1 580654 56645 22 542521 1.7 1 500784 41737 23 624224 1.7 1 570946 53278 24 590519 1.7 1 532912 57607 25 607047 1.7 1 556132 50915 26 572302 1.7 1 527531 44771 27 630635 1.7 1 573588 57047 28 620404 1.7 1 568899 51505 29 625305 1.7 1 567099 58206 30 664393 1.7 1 616071 48322 31 510018 1.7 1 469355 40663 32 637215 1.7 1 584852 52363 33 597607 1.7 1 545528 52079 34 753926 1.7 1 688559 65367 35 503645 1.7 1 462577 41068 36 630961 1.7 1 577612 53349 37 659262 1.7 1 604319 54943 38 595913 1.7 1 547877 48036 39 653746 1.7 1 597162 56584 40 670529 1.7 1 610664 59865 41 732564 1.7 1 667967 64597 42 545711 1.7 1 495424 50287 43 991735 1.7 1 924678 67057 44 286953 1.7 1 256328 30625 45 652219 1.7 1 601722 50497 46 619313 1.7 1 571113 48200 47 635341 1.7 1 585973 49368 48 610799 1.7 1 562441 48358 49 674495 1.7 1 617955 56540 50 598712 1.7 1 554202 44510 51 649220 1.7 1 598179 51041 52 650919 1.7 1 595866 55053 53 695670 1.7 1 642854 52816 54 545982 1.7 1 504022 41960 55 632591 1.7 1 583378 49213 56 771796 1.7 1 714466 57330 57 493419 1.7 1 450919 42500 58 643644 1.7 1 599707 43937 59 562738 1.7 1 517495 45243 60 620089 1.7 1 571985 48104 61 599005 1.7 1 554664 44341 62 665940 1.7 1 617471 48469 63 511736 1.7 1 469216 42520 64 570922 1.7 1 530032 40890 65 624134 1.7 1 576865 47269 66 644685 1.7 1 596010 48675 67 692204 1.7 1 630686 61518 68 1251198 1.7 1 1176122 75076 69 255502 1.7 1 232815 22687 70 102840 1.7 1 86533 16307 71 343135 1.7 1 318441 24694 72 484356 1.7 1 451690 32666 73 511359 1.7 1 476313 35046 74 501885 1.7 1 465645 36240 75 495613 1.7 1 458847 36766 76 482971 1.7 1 446569 36402 77 471725 1.7 1 437257 34468 78 457894 1.7 1 423781 34113 79 452070 1.7 1 418062 34008 80 438484 1.7 1 405088 33396 81 425410 1.7 1 393919 31491 82 414132 1.7 1 383041 31091 83 396751 1.7 1 367831 28920 84 386912 1.7 1 357963 28949 85 373056 1.7 1 345296 27760 86 351920 1.7 1 325697 26223 87 339788 1.7 1 315178 24610 88 331230 1.7 1 306931 24299 89 311047 1.7 1 288166 22881 90 302757 1.7 1 280581 22176 91 287473 1.7 1 266368 21105 92 274821 1.7 1 254675 20146 93 261527 1.7 1 242454 19073 94 247083 1.7 1 228486 18597 95 229569 1.7 1 212524 17045 96 215425 1.7 1 199345 16080 97 200580 1.7 1 186258 14322 98 186104 1.7 1 172508 13596 99 176938 1.7 1 163984 12954 100 163824 1.7 1 151757 12067 101 152410 1.7 1 141174 11236 102 139508 1.7 1 128964 10544 103 126668 1.7 1 117083 9585 104 114659 1.7 1 106240 8419 105 103515 1.7 1 95951 7564 106 93675 1.7 1 86344 7331 107 82801 1.7 1 76358 6443 108 74274 1.7 1 68589 5685 109 65750 1.7 1 60455 5295 110 58361 1.7 1 53718 4643 111 51503 1.7 1 47445 4058 112 46515 1.7 1 42704 3811 113 39788 1.7 1 36495 3293 114 35516 1.7 1 32502 3014 115 29286 1.7 1 26808 2478 116 25103 1.7 1 22972 2131 117 21040 1.7 1 19128 1912 118 17330 1.7 1 15763 1567 119 14917 1.7 1 13608 1309 120 12642 1.7 1 11544 1098 121 10638 1.7 1 9581 1057 122 8906 1.7 1 8053 853 123 7247 1.7 1 6562 685 124 6246 1.7 1 5598 648 125 5323 1.7 1 4772 551 126 5106 1.7 1 4581 525 127 4365 1.7 1 3924 441 128 3325 1.7 1 2922 403 129 2686 1.7 1 2381 305 130 3038 1.7 1 2747 291 131 4431 1.7 1 4079 352 132 5138 1.7 1 4758 380 133 6888 1.7 1 6396 492 134 9151 1.7 1 8614 537 135 3733 1.7 1 3470 263 136 1176 1.7 1 1019 157 137 621 1.7 1 528 93 138 473 1.7 1 413 60 139 304 1.7 1 257 47 140 204 1.7 1 168 36 141 175 1.7 1 143 32 142 95 1.7 1 74 21 143 82 1.7 1 66 16 144 113 1.7 1 89 24 145 229 1.7 1 203 26 146 212 1.7 1 174 38 147 863 1.7 1 726 137 148 473 1.7 1 383 90 149 260 1.7 1 220 40 150 2364 1.7 1 1963 401 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L002_R1_001.fastq.gz ============================================= 112706276 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 37209 (0.0%)