SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_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_F2_S22_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 3850.13 s (47 us/read; 1.28 M reads/minute). === Summary === Total reads processed: 82,177,525 Reads with adapters: 58,336,382 (71.0%) Reads written (passing filters): 82,177,525 (100.0%) Total basepairs processed: 12,326,628,750 bp Quality-trimmed: 41,419,626 bp (0.3%) Total written (filtered): 10,364,431,817 bp (84.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58336382 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: 34.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15350057 20544381.2 0 15350057 2 1685474 5136095.3 0 1685474 3 903882 1284023.8 0 903882 4 571222 321006.0 0 571222 5 501936 80251.5 0 501936 6 415827 20062.9 0 415827 7 347542 5015.7 0 347542 8 483968 1253.9 0 483968 9 396796 313.5 0 395692 1104 10 420274 78.4 1 402160 18114 11 438864 19.6 1 414608 24256 12 449536 4.9 1 424165 25371 13 510213 1.2 1 482515 27698 14 455618 1.2 1 427602 28016 15 389210 1.2 1 366432 22778 16 555171 1.2 1 523342 31829 17 419400 1.2 1 394087 25313 18 418646 1.2 1 395171 23475 19 509488 1.2 1 480141 29347 20 480908 1.2 1 453798 27110 21 427296 1.2 1 402705 24591 22 474401 1.2 1 448452 25949 23 490252 1.2 1 461826 28426 24 484904 1.2 1 457572 27332 25 539104 1.2 1 510128 28976 26 453073 1.2 1 425411 27662 27 501857 1.2 1 468630 33227 28 457877 1.2 1 436189 21688 29 491156 1.2 1 462299 28857 30 462417 1.2 1 439850 22567 31 522905 1.2 1 492898 30007 32 460424 1.2 1 437863 22561 33 512386 1.2 1 483241 29145 34 657426 1.2 1 620019 37407 35 363385 1.2 1 345024 18361 36 487371 1.2 1 459211 28160 37 533683 1.2 1 504069 29614 38 481104 1.2 1 458652 22452 39 485376 1.2 1 462217 23159 40 532302 1.2 1 503234 29068 41 511389 1.2 1 485806 25583 42 521546 1.2 1 495601 25945 43 480650 1.2 1 455868 24782 44 546125 1.2 1 517755 28370 45 570120 1.2 1 542069 28051 46 418884 1.2 1 397786 21098 47 505326 1.2 1 481272 24054 48 488484 1.2 1 466397 22087 49 514214 1.2 1 489094 25120 50 501739 1.2 1 476010 25729 51 610289 1.2 1 580951 29338 52 441047 1.2 1 421068 19979 53 520314 1.2 1 497213 23101 54 398195 1.2 1 379916 18279 55 496805 1.2 1 475323 21482 56 496057 1.2 1 473000 23057 57 480165 1.2 1 458650 21515 58 465002 1.2 1 445044 19958 59 473368 1.2 1 452197 21171 60 477456 1.2 1 455816 21640 61 491054 1.2 1 468379 22675 62 525084 1.2 1 500148 24936 63 688105 1.2 1 659460 28645 64 513363 1.2 1 493656 19707 65 351437 1.2 1 336316 15121 66 388237 1.2 1 371824 16413 67 391608 1.2 1 373999 17609 68 389520 1.2 1 372639 16881 69 387449 1.2 1 370434 17015 70 386662 1.2 1 369736 16926 71 401493 1.2 1 384632 16861 72 387884 1.2 1 370945 16939 73 410793 1.2 1 393742 17051 74 371310 1.2 1 356033 15277 75 357117 1.2 1 342286 14831 76 343694 1.2 1 329251 14443 77 331451 1.2 1 317224 14227 78 322073 1.2 1 308399 13674 79 311753 1.2 1 298772 12981 80 303996 1.2 1 291594 12402 81 292352 1.2 1 280150 12202 82 283173 1.2 1 271407 11766 83 268006 1.2 1 256925 11081 84 264798 1.2 1 253456 11342 85 258296 1.2 1 247093 11203 86 251541 1.2 1 240826 10715 87 251948 1.2 1 241533 10415 88 239999 1.2 1 230066 9933 89 210279 1.2 1 201522 8757 90 198432 1.2 1 189963 8469 91 186654 1.2 1 178634 8020 92 175644 1.2 1 168171 7473 93 173446 1.2 1 166287 7159 94 161637 1.2 1 154843 6794 95 151052 1.2 1 144859 6193 96 140237 1.2 1 134508 5729 97 130886 1.2 1 125542 5344 98 122501 1.2 1 117472 5029 99 115054 1.2 1 110586 4468 100 107801 1.2 1 103547 4254 101 95638 1.2 1 91917 3721 102 87834 1.2 1 84365 3469 103 80762 1.2 1 77514 3248 104 75976 1.2 1 73089 2887 105 67619 1.2 1 64884 2735 106 60836 1.2 1 58481 2355 107 52108 1.2 1 50074 2034 108 45224 1.2 1 43372 1852 109 41239 1.2 1 39535 1704 110 35967 1.2 1 34472 1495 111 33060 1.2 1 31766 1294 112 29404 1.2 1 28175 1229 113 24708 1.2 1 23673 1035 114 22438 1.2 1 21537 901 115 17752 1.2 1 17001 751 116 15010 1.2 1 14377 633 117 12079 1.2 1 11520 559 118 10437 1.2 1 9967 470 119 8208 1.2 1 7826 382 120 7212 1.2 1 6891 321 121 6273 1.2 1 5988 285 122 5055 1.2 1 4818 237 123 4309 1.2 1 4110 199 124 3571 1.2 1 3389 182 125 2948 1.2 1 2833 115 126 2296 1.2 1 2182 114 127 1959 1.2 1 1851 108 128 1542 1.2 1 1473 69 129 1221 1.2 1 1160 61 130 1047 1.2 1 984 63 131 945 1.2 1 892 53 132 678 1.2 1 641 37 133 631 1.2 1 593 38 134 648 1.2 1 616 32 135 387 1.2 1 364 23 136 258 1.2 1 239 19 137 195 1.2 1 184 11 138 163 1.2 1 151 12 139 116 1.2 1 108 8 140 92 1.2 1 83 9 141 73 1.2 1 63 10 142 63 1.2 1 54 9 143 46 1.2 1 37 9 144 54 1.2 1 48 6 145 44 1.2 1 35 9 146 46 1.2 1 42 4 147 78 1.2 1 75 3 148 63 1.2 1 57 6 149 48 1.2 1 46 2 150 297 1.2 1 280 17 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F2_S22_L001_R2_001.fastq.gz ============================================= 82177525 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 73881 (0.1%)