SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_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_F2_S22_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 3673.76 s (45 us/read; 1.33 M reads/minute). === Summary === Total reads processed: 81,699,034 Reads with adapters: 58,422,606 (71.5%) Reads written (passing filters): 81,699,034 (100.0%) Total basepairs processed: 12,254,855,100 bp Quality-trimmed: 19,487,828 bp (0.2%) Total written (filtered): 10,283,682,296 bp (83.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58422606 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.4% C: 11.4% G: 19.4% T: 33.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15199129 20424758.5 0 15199129 2 1580922 5106189.6 0 1580922 3 842043 1276547.4 0 842043 4 550022 319136.9 0 550022 5 449997 79784.2 0 449997 6 434481 19946.1 0 434481 7 347898 4986.5 0 347898 8 441084 1246.6 0 441084 9 443045 311.7 0 438482 4563 10 405413 77.9 1 382098 23315 11 450388 19.5 1 415672 34716 12 442770 4.9 1 412586 30184 13 446024 1.2 1 415108 30916 14 453376 1.2 1 419388 33988 15 468278 1.2 1 435263 33015 16 452666 1.2 1 416929 35737 17 549238 1.2 1 503600 45638 18 466886 1.2 1 435945 30941 19 393788 1.2 1 366567 27221 20 467902 1.2 1 436166 31736 21 521792 1.2 1 483620 38172 22 433680 1.2 1 406255 27425 23 504819 1.2 1 468719 36100 24 475517 1.2 1 437053 38464 25 491820 1.2 1 457067 34753 26 461178 1.2 1 431235 29943 27 512653 1.2 1 473769 38884 28 491651 1.2 1 457681 33970 29 512510 1.2 1 470963 41547 30 548141 1.2 1 514010 34131 31 409025 1.2 1 380832 28193 32 540631 1.2 1 502491 38140 33 452892 1.2 1 421055 31837 34 512380 1.2 1 471655 40725 35 569764 1.2 1 523370 46394 36 519856 1.2 1 484148 35708 37 553142 1.2 1 519802 33340 38 400544 1.2 1 364810 35734 39 573002 1.2 1 528499 44503 40 466836 1.2 1 435154 31682 41 600726 1.2 1 554364 46362 42 453939 1.2 1 416218 37721 43 790864 1.2 1 744421 46443 44 241028 1.2 1 218439 22589 45 522905 1.2 1 486598 36307 46 536313 1.2 1 498381 37932 47 536772 1.2 1 501509 35263 48 445960 1.2 1 412336 33624 49 569976 1.2 1 527084 42892 50 451713 1.2 1 423569 28144 51 503554 1.2 1 469351 34203 52 559241 1.2 1 515373 43868 53 626961 1.2 1 588950 38011 54 397202 1.2 1 368180 29022 55 510273 1.2 1 477059 33214 56 566018 1.2 1 530313 35705 57 490065 1.2 1 455879 34186 58 448852 1.2 1 423488 25364 59 352650 1.2 1 326693 25957 60 521343 1.2 1 488341 33002 61 489445 1.2 1 459888 29557 62 454351 1.2 1 425498 28853 63 442859 1.2 1 412719 30140 64 413454 1.2 1 388538 24916 65 428487 1.2 1 400331 28156 66 475641 1.2 1 444595 31046 67 527546 1.2 1 487484 40062 68 932793 1.2 1 883259 49534 69 306211 1.2 1 285490 20721 70 98330 1.2 1 86452 11878 71 183213 1.2 1 170097 13116 72 347828 1.2 1 327310 20518 73 384493 1.2 1 361546 22947 74 375434 1.2 1 351755 23679 75 372810 1.2 1 349151 23659 76 366345 1.2 1 341732 24613 77 349631 1.2 1 326987 22644 78 336085 1.2 1 313727 22358 79 334791 1.2 1 312735 22056 80 320766 1.2 1 299322 21444 81 308813 1.2 1 288662 20151 82 303376 1.2 1 282871 20505 83 287613 1.2 1 268884 18729 84 281524 1.2 1 262646 18878 85 269523 1.2 1 251601 17922 86 255982 1.2 1 238963 17019 87 246467 1.2 1 230371 16096 88 240096 1.2 1 224172 15924 89 222064 1.2 1 207380 14684 90 214626 1.2 1 200391 14235 91 204511 1.2 1 191212 13299 92 193574 1.2 1 180679 12895 93 185417 1.2 1 173008 12409 94 174914 1.2 1 163234 11680 95 159670 1.2 1 148732 10938 96 150695 1.2 1 140365 10330 97 140751 1.2 1 131592 9159 98 129553 1.2 1 120450 9103 99 122439 1.2 1 114105 8334 100 113910 1.2 1 106001 7909 101 103551 1.2 1 96319 7232 102 95288 1.2 1 88666 6622 103 86137 1.2 1 80145 5992 104 77327 1.2 1 71858 5469 105 69993 1.2 1 65045 4948 106 63171 1.2 1 58489 4682 107 54679 1.2 1 50722 3957 108 49406 1.2 1 45775 3631 109 44550 1.2 1 41176 3374 110 38825 1.2 1 35771 3054 111 33501 1.2 1 30848 2653 112 30928 1.2 1 28428 2500 113 25660 1.2 1 23574 2086 114 23733 1.2 1 21729 2004 115 19374 1.2 1 17711 1663 116 16667 1.2 1 15185 1482 117 13526 1.2 1 12278 1248 118 11411 1.2 1 10398 1013 119 9123 1.2 1 8243 880 120 8085 1.2 1 7320 765 121 6821 1.2 1 6153 668 122 5630 1.2 1 5011 619 123 4598 1.2 1 4108 490 124 3796 1.2 1 3390 406 125 3140 1.2 1 2802 338 126 2509 1.2 1 2205 304 127 2125 1.2 1 1865 260 128 1671 1.2 1 1452 219 129 1329 1.2 1 1142 187 130 1120 1.2 1 991 129 131 940 1.2 1 808 132 132 761 1.2 1 666 95 133 675 1.2 1 585 90 134 682 1.2 1 604 78 135 447 1.2 1 388 59 136 330 1.2 1 286 44 137 223 1.2 1 175 48 138 187 1.2 1 160 27 139 149 1.2 1 117 32 140 100 1.2 1 80 20 141 64 1.2 1 50 14 142 63 1.2 1 51 12 143 43 1.2 1 29 14 144 41 1.2 1 32 9 145 44 1.2 1 36 8 146 35 1.2 1 24 11 147 75 1.2 1 69 6 148 65 1.2 1 52 13 149 34 1.2 1 28 6 150 405 1.2 1 345 60 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L002_R1_001.fastq.gz ============================================= 81699034 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 5455 (0.0%)