SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L001_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_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 3621.61 s (44 us/read; 1.36 M reads/minute). === Summary === Total reads processed: 82,177,525 Reads with adapters: 58,714,265 (71.4%) Reads written (passing filters): 82,177,525 (100.0%) Total basepairs processed: 12,326,628,750 bp Quality-trimmed: 17,863,332 bp (0.1%) Total written (filtered): 10,356,260,345 bp (84.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58714265 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.4% C: 11.4% G: 19.3% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15334703 20544381.2 0 15334703 2 1608191 5136095.3 0 1608191 3 847327 1284023.8 0 847327 4 558993 321006.0 0 558993 5 451836 80251.5 0 451836 6 436528 20062.9 0 436528 7 362332 5015.7 0 362332 8 445624 1253.9 0 445624 9 448853 313.5 0 444071 4782 10 414974 78.4 1 395643 19331 11 451608 19.6 1 421964 29644 12 446668 4.9 1 421394 25274 13 448758 1.2 1 423173 25585 14 458328 1.2 1 429437 28891 15 470816 1.2 1 443807 27009 16 459713 1.2 1 429546 30167 17 546940 1.2 1 508999 37941 18 471227 1.2 1 445754 25473 19 402058 1.2 1 378920 23138 20 471685 1.2 1 445002 26683 21 519729 1.2 1 487230 32499 22 441834 1.2 1 419209 22625 23 505202 1.2 1 475325 29877 24 480556 1.2 1 445808 34748 25 495463 1.2 1 465784 29679 26 468036 1.2 1 442448 25588 27 512154 1.2 1 478482 33672 28 492492 1.2 1 462349 30143 29 513596 1.2 1 476912 36684 30 549763 1.2 1 521613 28150 31 416541 1.2 1 392371 24170 32 537990 1.2 1 507240 30750 33 461062 1.2 1 434172 26890 34 514898 1.2 1 482060 32838 35 565682 1.2 1 527137 38545 36 520514 1.2 1 491038 29476 37 563159 1.2 1 535989 27170 38 400017 1.2 1 369694 30323 39 571304 1.2 1 535130 36174 40 474621 1.2 1 448623 25998 41 600561 1.2 1 562019 38542 42 458766 1.2 1 426402 32364 43 800955 1.2 1 763696 37259 44 235002 1.2 1 215582 19420 45 521706 1.2 1 491650 30056 46 537461 1.2 1 505916 31545 47 540258 1.2 1 510434 29824 48 449883 1.2 1 420809 29074 49 566867 1.2 1 529971 36896 50 457025 1.2 1 432856 24169 51 503689 1.2 1 474572 29117 52 554879 1.2 1 516852 38027 53 630277 1.2 1 598162 32115 54 395812 1.2 1 371351 24461 55 516387 1.2 1 488413 27974 56 554072 1.2 1 525098 28974 57 493826 1.2 1 465005 28821 58 455432 1.2 1 435241 20191 59 348004 1.2 1 326224 21780 60 524024 1.2 1 495485 28539 61 494677 1.2 1 470013 24664 62 445581 1.2 1 422101 23480 63 440868 1.2 1 415824 25044 64 419014 1.2 1 397741 21273 65 430484 1.2 1 407046 23438 66 478836 1.2 1 451552 27284 67 526917 1.2 1 490973 35944 68 974235 1.2 1 930569 43666 69 263384 1.2 1 246743 16641 70 78060 1.2 1 68230 9830 71 188944 1.2 1 177000 11944 72 350249 1.2 1 331713 18536 73 385004 1.2 1 364669 20335 74 373731 1.2 1 353304 20427 75 372636 1.2 1 352683 19953 76 364052 1.2 1 344608 19444 77 349658 1.2 1 330711 18947 78 336268 1.2 1 317764 18504 79 333907 1.2 1 315525 18382 80 320027 1.2 1 302554 17473 81 308343 1.2 1 291381 16962 82 303079 1.2 1 286638 16441 83 285198 1.2 1 269542 15656 84 281618 1.2 1 266189 15429 85 270078 1.2 1 255167 14911 86 256741 1.2 1 242477 14264 87 246300 1.2 1 232699 13601 88 239359 1.2 1 226087 13272 89 221157 1.2 1 208813 12344 90 214943 1.2 1 202774 12169 91 203469 1.2 1 192053 11416 92 193081 1.2 1 182042 11039 93 185749 1.2 1 175077 10672 94 173524 1.2 1 163677 9847 95 160182 1.2 1 150706 9476 96 148958 1.2 1 140034 8924 97 139705 1.2 1 131505 8200 98 129444 1.2 1 121874 7570 99 121244 1.2 1 114040 7204 100 113165 1.2 1 106483 6682 101 102845 1.2 1 96512 6333 102 94108 1.2 1 88374 5734 103 85449 1.2 1 80229 5220 104 76917 1.2 1 72056 4861 105 69454 1.2 1 64912 4542 106 62657 1.2 1 58630 4027 107 54683 1.2 1 51109 3574 108 49110 1.2 1 45908 3202 109 44137 1.2 1 41058 3079 110 38372 1.2 1 35617 2755 111 33619 1.2 1 31136 2483 112 30434 1.2 1 28239 2195 113 25366 1.2 1 23490 1876 114 23496 1.2 1 21717 1779 115 19033 1.2 1 17590 1443 116 16344 1.2 1 14972 1372 117 13454 1.2 1 12326 1128 118 11466 1.2 1 10507 959 119 8924 1.2 1 8136 788 120 8008 1.2 1 7309 699 121 6748 1.2 1 6146 602 122 5464 1.2 1 4939 525 123 4525 1.2 1 4074 451 124 3864 1.2 1 3437 427 125 3136 1.2 1 2820 316 126 2478 1.2 1 2171 307 127 2123 1.2 1 1865 258 128 1659 1.2 1 1463 196 129 1306 1.2 1 1161 145 130 1169 1.2 1 1027 142 131 997 1.2 1 875 122 132 756 1.2 1 652 104 133 674 1.2 1 579 95 134 665 1.2 1 580 85 135 442 1.2 1 374 68 136 281 1.2 1 246 35 137 223 1.2 1 178 45 138 175 1.2 1 145 30 139 132 1.2 1 108 24 140 105 1.2 1 88 17 141 84 1.2 1 61 23 142 69 1.2 1 59 10 143 49 1.2 1 38 11 144 68 1.2 1 56 12 145 42 1.2 1 31 11 146 49 1.2 1 40 9 147 75 1.2 1 67 8 148 68 1.2 1 58 10 149 58 1.2 1 50 8 150 375 1.2 1 309 66 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L001_R1_001.fastq.gz ============================================= 82177525 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 5465 (0.0%)