SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L001_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_F1_S20_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 5296.87 s (47 us/read; 1.29 M reads/minute). === Summary === Total reads processed: 113,474,961 Reads with adapters: 79,235,271 (69.8%) Reads written (passing filters): 113,474,961 (100.0%) Total basepairs processed: 17,021,244,150 bp Quality-trimmed: 73,052,751 bp (0.4%) Total written (filtered): 14,433,737,028 bp (84.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 79235271 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.2% C: 9.2% G: 21.3% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24292490 28368740.2 0 24292490 2 2172289 7092185.1 0 2172289 3 1212765 1773046.3 0 1212765 4 728934 443261.6 0 728934 5 615953 110815.4 0 615953 6 518496 27703.8 0 518496 7 424176 6926.0 0 424176 8 595932 1731.5 0 595932 9 493164 432.9 0 491188 1976 10 515557 108.2 1 490642 24915 11 544480 27.1 1 510284 34196 12 557302 6.8 1 522559 34743 13 624852 1.7 1 586293 38559 14 566086 1.7 1 527536 38550 15 479671 1.7 1 447634 32037 16 677197 1.7 1 634485 42712 17 518178 1.7 1 482968 35210 18 513709 1.7 1 481055 32654 19 623697 1.7 1 583105 40592 20 590778 1.7 1 553837 36941 21 523012 1.7 1 489156 33856 22 582166 1.7 1 546634 35532 23 607194 1.7 1 567433 39761 24 596018 1.7 1 558835 37183 25 658603 1.7 1 618497 40106 26 563795 1.7 1 525767 38028 27 625280 1.7 1 580031 45249 28 565755 1.7 1 537011 28744 29 604057 1.7 1 566572 37485 30 575342 1.7 1 545309 30033 31 637117 1.7 1 598679 38438 32 567491 1.7 1 538376 29115 33 633139 1.7 1 594872 38267 34 807925 1.7 1 759853 48072 35 450122 1.7 1 426055 24067 36 611610 1.7 1 574682 36928 37 655880 1.7 1 616910 38970 38 600986 1.7 1 571449 29537 39 595629 1.7 1 565252 30377 40 651655 1.7 1 614241 37414 41 634336 1.7 1 600514 33822 42 641088 1.7 1 607660 33428 43 603840 1.7 1 570768 33072 44 681587 1.7 1 644069 37518 45 707281 1.7 1 670903 36378 46 517703 1.7 1 489820 27883 47 633055 1.7 1 601375 31680 48 613751 1.7 1 584361 29390 49 644336 1.7 1 611009 33327 50 626710 1.7 1 592951 33759 51 770564 1.7 1 731245 39319 52 552184 1.7 1 525737 26447 53 655644 1.7 1 624724 30920 54 497055 1.7 1 473150 23905 55 622404 1.7 1 594084 28320 56 630771 1.7 1 599636 31135 57 608401 1.7 1 579359 29042 58 589791 1.7 1 563588 26203 59 602895 1.7 1 574430 28465 60 610621 1.7 1 581075 29546 61 631221 1.7 1 600250 30971 62 678983 1.7 1 645436 33547 63 884166 1.7 1 845237 38929 64 697534 1.7 1 670069 27465 65 461327 1.7 1 440187 21140 66 505461 1.7 1 482444 23017 67 504336 1.7 1 480520 23816 68 506997 1.7 1 484099 22898 69 501262 1.7 1 477906 23356 70 506318 1.7 1 482633 23685 71 530040 1.7 1 506417 23623 72 512724 1.7 1 488940 23784 73 535324 1.7 1 511542 23782 74 491314 1.7 1 470184 21130 75 468392 1.7 1 447958 20434 76 453588 1.7 1 433629 19959 77 443997 1.7 1 423454 20543 78 435469 1.7 1 416134 19335 79 419163 1.7 1 400603 18560 80 414024 1.7 1 395828 18196 81 398372 1.7 1 381040 17332 82 382299 1.7 1 365451 16848 83 366779 1.7 1 350673 16106 84 355643 1.7 1 339567 16076 85 348592 1.7 1 332671 15921 86 340981 1.7 1 325646 15335 87 343724 1.7 1 328719 15005 88 328419 1.7 1 314072 14347 89 293572 1.7 1 280847 12725 90 277907 1.7 1 265475 12432 91 261801 1.7 1 250188 11613 92 247933 1.7 1 237089 10844 93 241002 1.7 1 230436 10566 94 225907 1.7 1 216109 9798 95 212543 1.7 1 203112 9431 96 199922 1.7 1 191511 8411 97 189942 1.7 1 181742 8200 98 181068 1.7 1 173356 7712 99 177800 1.7 1 170721 7079 100 161532 1.7 1 154936 6596 101 142590 1.7 1 136815 5775 102 127109 1.7 1 121824 5285 103 114820 1.7 1 109872 4948 104 106755 1.7 1 102353 4402 105 97032 1.7 1 93102 3930 106 87939 1.7 1 84311 3628 107 77043 1.7 1 73799 3244 108 66878 1.7 1 63922 2956 109 60697 1.7 1 58149 2548 110 53817 1.7 1 51530 2287 111 49656 1.7 1 47564 2092 112 44212 1.7 1 42328 1884 113 37568 1.7 1 35930 1638 114 33504 1.7 1 32034 1470 115 26873 1.7 1 25557 1316 116 23021 1.7 1 21918 1103 117 18702 1.7 1 17804 898 118 15710 1.7 1 14954 756 119 13467 1.7 1 12827 640 120 11166 1.7 1 10610 556 121 9578 1.7 1 9044 534 122 7970 1.7 1 7515 455 123 6749 1.7 1 6389 360 124 5790 1.7 1 5438 352 125 4982 1.7 1 4674 308 126 4691 1.7 1 4415 276 127 3926 1.7 1 3689 237 128 2937 1.7 1 2717 220 129 2589 1.7 1 2397 192 130 2951 1.7 1 2762 189 131 4241 1.7 1 4050 191 132 4816 1.7 1 4604 212 133 7287 1.7 1 6984 303 134 8892 1.7 1 8589 303 135 3540 1.7 1 3386 154 136 1144 1.7 1 1071 73 137 598 1.7 1 565 33 138 406 1.7 1 369 37 139 302 1.7 1 277 25 140 227 1.7 1 197 30 141 147 1.7 1 128 19 142 76 1.7 1 62 14 143 79 1.7 1 62 17 144 94 1.7 1 81 13 145 260 1.7 1 229 31 146 164 1.7 1 145 19 147 597 1.7 1 528 69 148 305 1.7 1 255 50 149 176 1.7 1 150 26 150 1321 1.7 1 1192 129 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L001_R2_001.fastq.gz ============================================= 113474961 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 164893 (0.1%)