SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_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_F1_S20_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 5053.89 s (45 us/read; 1.35 M reads/minute). === Summary === Total reads processed: 113,474,961 Reads with adapters: 78,847,369 (69.5%) Reads written (passing filters): 113,474,961 (100.0%) Total basepairs processed: 17,021,244,150 bp Quality-trimmed: 22,715,789 bp (0.1%) Total written (filtered): 14,426,732,983 bp (84.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 78847369 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.1% C: 9.7% G: 19.7% T: 34.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22838934 28368740.2 0 22838934 2 2342589 7092185.1 0 2342589 3 1202279 1773046.3 0 1202279 4 750593 443261.6 0 750593 5 559528 110815.4 0 559528 6 524826 27703.8 0 524826 7 449332 6926.0 0 449332 8 548899 1731.5 0 548899 9 548856 432.9 0 541308 7548 10 508456 108.2 1 478983 29473 11 562956 27.1 1 517668 45288 12 559587 6.8 1 520090 39497 13 547304 1.7 1 508519 38785 14 570426 1.7 1 525734 44692 15 575858 1.7 1 534867 40991 16 569860 1.7 1 523134 46726 17 678914 1.7 1 621846 57068 18 565739 1.7 1 526451 39288 19 504906 1.7 1 468246 36660 20 580103 1.7 1 539012 41091 21 633303 1.7 1 584154 49149 22 551495 1.7 1 516023 35472 23 623244 1.7 1 577696 45548 24 597040 1.7 1 545080 51960 25 610942 1.7 1 565949 44993 26 578327 1.7 1 539305 39022 27 631060 1.7 1 581266 49794 28 620380 1.7 1 573987 46393 29 630417 1.7 1 577901 52516 30 665372 1.7 1 624016 41356 31 521479 1.7 1 485824 35655 32 637552 1.7 1 593972 43580 33 605503 1.7 1 560522 44981 34 753213 1.7 1 699064 54149 35 512573 1.7 1 477265 35308 36 633868 1.7 1 587959 45909 37 659372 1.7 1 612861 46511 38 603868 1.7 1 563307 40561 39 656560 1.7 1 609454 47106 40 670911 1.7 1 620635 50276 41 733444 1.7 1 678908 54536 42 554355 1.7 1 510902 43453 43 1004589 1.7 1 949034 55555 44 281497 1.7 1 254795 26702 45 650424 1.7 1 607820 42604 46 622059 1.7 1 580617 41442 47 641812 1.7 1 599651 42161 48 616364 1.7 1 574406 41958 49 673245 1.7 1 623804 49441 50 604428 1.7 1 565417 39011 51 645021 1.7 1 600411 44610 52 648661 1.7 1 600394 48267 53 693327 1.7 1 647436 45891 54 550715 1.7 1 514274 36441 55 631316 1.7 1 588270 43046 56 767345 1.7 1 719044 48301 57 493710 1.7 1 456524 37186 58 647241 1.7 1 610352 36889 59 560612 1.7 1 522206 38406 60 620281 1.7 1 578774 41507 61 603855 1.7 1 565232 38623 62 664795 1.7 1 623425 41370 63 508452 1.7 1 471688 36764 64 573553 1.7 1 538426 35127 65 625525 1.7 1 584793 40732 66 654791 1.7 1 611542 43249 67 693655 1.7 1 637398 56257 68 1295847 1.7 1 1228868 66979 69 207198 1.7 1 188952 18246 70 83872 1.7 1 69823 14049 71 351217 1.7 1 328576 22641 72 486564 1.7 1 456539 30025 73 511552 1.7 1 479835 31717 74 500225 1.7 1 468801 31424 75 493734 1.7 1 462637 31097 76 485479 1.7 1 455415 30064 77 472130 1.7 1 442425 29705 78 457249 1.7 1 427856 29393 79 452598 1.7 1 423758 28840 80 436888 1.7 1 409466 27422 81 424029 1.7 1 397325 26704 82 413331 1.7 1 387262 26069 83 395648 1.7 1 370721 24927 84 386472 1.7 1 362163 24309 85 373564 1.7 1 350510 23054 86 350177 1.7 1 327542 22635 87 338817 1.7 1 317459 21358 88 329564 1.7 1 308892 20672 89 310326 1.7 1 290522 19804 90 302165 1.7 1 282977 19188 91 286619 1.7 1 268441 18178 92 275091 1.7 1 257788 17303 93 261850 1.7 1 245237 16613 94 246459 1.7 1 230780 15679 95 229270 1.7 1 214573 14697 96 213682 1.7 1 200015 13667 97 200167 1.7 1 187352 12815 98 186673 1.7 1 174782 11891 99 177389 1.7 1 165973 11416 100 164170 1.7 1 153549 10621 101 152020 1.7 1 142083 9937 102 138827 1.7 1 129592 9235 103 126885 1.7 1 118589 8296 104 114180 1.7 1 106471 7709 105 103407 1.7 1 96323 7084 106 93053 1.7 1 86648 6405 107 82305 1.7 1 76807 5498 108 73960 1.7 1 68774 5186 109 66073 1.7 1 61323 4750 110 58316 1.7 1 54124 4192 111 51210 1.7 1 47563 3647 112 46457 1.7 1 43051 3406 113 39166 1.7 1 36179 2987 114 35653 1.7 1 32939 2714 115 29363 1.7 1 27078 2285 116 25352 1.7 1 23356 1996 117 20912 1.7 1 19235 1677 118 17421 1.7 1 15974 1447 119 14864 1.7 1 13576 1288 120 12650 1.7 1 11578 1072 121 10471 1.7 1 9498 973 122 8802 1.7 1 7972 830 123 7467 1.7 1 6769 698 124 6267 1.7 1 5666 601 125 5296 1.7 1 4740 556 126 5081 1.7 1 4533 548 127 4350 1.7 1 3958 392 128 3255 1.7 1 2949 306 129 2684 1.7 1 2428 256 130 3108 1.7 1 2815 293 131 4344 1.7 1 4012 332 132 4969 1.7 1 4639 330 133 7178 1.7 1 6729 449 134 9066 1.7 1 8514 552 135 3718 1.7 1 3456 262 136 1190 1.7 1 1067 123 137 629 1.7 1 542 87 138 481 1.7 1 425 56 139 351 1.7 1 310 41 140 237 1.7 1 196 41 141 164 1.7 1 133 31 142 89 1.7 1 63 26 143 91 1.7 1 63 28 144 96 1.7 1 72 24 145 237 1.7 1 190 47 146 222 1.7 1 196 26 147 852 1.7 1 739 113 148 478 1.7 1 374 104 149 260 1.7 1 214 46 150 2350 1.7 1 1965 385 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L001_R1_001.fastq.gz ============================================= 113474961 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 37240 (0.0%)