SUMMARISING RUN PARAMETERS ========================== Input filename: larvae_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.7 Cutadapt version: 3.4 Python version: could not detect Number of cores used for trimming: 4 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 1754). Second best hit was smallRNA (count: 8) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 2-colour high quality G-trimming enabled, with quality cutoff: --nextseq-trim=20 Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 3.4 with Python 3.9.6 Command line parameters: -j 4 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC larvae_2.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 769.98 s (11 µs/read; 5.69 M reads/minute). === Summary === Total reads processed: 72,973,389 Reads with adapters: 22,435,944 (30.7%) Reads written (passing filters): 72,973,389 (100.0%) Total basepairs processed: 10,585,470,773 bp Quality-trimmed: 269,827,755 bp (2.5%) Total written (filtered): 10,195,205,337 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22435944 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.9% C: 24.5% G: 16.0% T: 20.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18252965 18243347.2 0 18252965 3 1225659 1140209.2 0 1225659 4 378394 285052.3 0 378394 5 226390 71263.1 0 226390 8 72178 1113.5 0 72178 9 85673 278.4 0 85673 10 945 69.6 1 0 945 11 101356 17.4 1 88882 12474 12 1685 4.3 1 0 1685 13 126763 1.1 1 104793 21970 14 3182 1.1 1 508 2674 15 41576 1.1 1 36193 5383 16 168572 1.1 1 146571 22001 17 4372 1.1 1 1568 2804 18 102139 1.1 1 93473 8666 19 4101 1.1 1 2013 2088 20 75234 1.1 1 67811 7423 21 228345 1.1 1 213084 15261 22 5567 1.1 1 3395 2172 23 560 1.1 1 407 153 24 1548 1.1 1 1029 519 25 76542 1.1 1 71014 5528 26 101699 1.1 1 93415 8284 27 132032 1.1 1 123130 8902 28 4173 1.1 1 2986 1187 29 73683 1.1 1 68582 5101 30 4723 1.1 1 3452 1271 31 105616 1.1 1 100918 4698 32 10221 1.1 1 7868 2353 33 51479 1.1 1 47567 3912 34 34489 1.1 1 30329 4160 35 1148 1.1 1 842 306 36 8513 1.1 1 7252 1261 37 34395 1.1 1 32115 2280 38 6219 1.1 1 4993 1226 39 23329 1.1 1 20839 2490 40 16107 1.1 1 13540 2567 41 4031 1.1 1 2902 1129 42 2354 1.1 1 1834 520 43 8434 1.1 1 7146 1288 44 2363 1.1 1 1629 734 45 734 1.1 1 533 201 46 5508 1.1 1 4589 919 47 2721 1.1 1 1902 819 48 2267 1.1 1 1636 631 49 3583 1.1 1 2768 815 50 4876 1.1 1 3831 1045 51 2355 1.1 1 1720 635 52 863 1.1 1 633 230 53 1625 1.1 1 1252 373 54 2668 1.1 1 2185 483 55 1884 1.1 1 1342 542 56 2686 1.1 1 1998 688 57 2335 1.1 1 1850 485 58 3462 1.1 1 2868 594 59 2190 1.1 1 1627 563 60 2115 1.1 1 1629 486 61 2298 1.1 1 1789 509 62 2509 1.1 1 1800 709 63 2462 1.1 1 1812 650 64 1737 1.1 1 1165 572 65 1389 1.1 1 643 746 66 1654 1.1 1 540 1114 67 24158 1.1 1 762 23396 68 54652 1.1 1 797 53855 69 41318 1.1 1 693 40625 70 51753 1.1 1 650 51103 71 36966 1.1 1 461 36505 72 27491 1.1 1 365 27126 73 17516 1.1 1 311 17205 74 13540 1.1 1 235 13305 75 14075 1.1 1 161 13914 76 9264 1.1 1 144 9120 77 7450 1.1 1 125 7325 78 8016 1.1 1 105 7911 79 7652 1.1 1 91 7561 80 9408 1.1 1 78 9330 81 8596 1.1 1 77 8519 82 7485 1.1 1 102 7383 83 6312 1.1 1 85 6227 84 5513 1.1 1 80 5433 85 4859 1.1 1 60 4799 86 3476 1.1 1 62 3414 87 3263 1.1 1 62 3201 88 2809 1.1 1 64 2745 89 2301 1.1 1 49 2252 90 2063 1.1 1 52 2011 91 1850 1.1 1 45 1805 92 1418 1.1 1 66 1352 93 1300 1.1 1 43 1257 94 1140 1.1 1 38 1102 95 1056 1.1 1 38 1018 96 960 1.1 1 34 926 97 966 1.1 1 36 930 98 845 1.1 1 44 801 99 728 1.1 1 26 702 100 769 1.1 1 40 729 101 737 1.1 1 39 698 102 715 1.1 1 42 673 103 722 1.1 1 52 670 104 792 1.1 1 40 752 105 773 1.1 1 42 731 106 813 1.1 1 30 783 107 903 1.1 1 34 869 108 1055 1.1 1 33 1022 109 1129 1.1 1 33 1096 110 1170 1.1 1 39 1131 111 1187 1.1 1 40 1147 112 1255 1.1 1 39 1216 113 1267 1.1 1 38 1229 114 1147 1.1 1 33 1114 115 1109 1.1 1 29 1080 116 1008 1.1 1 25 983 117 994 1.1 1 36 958 118 975 1.1 1 34 941 119 760 1.1 1 37 723 120 734 1.1 1 17 717 121 712 1.1 1 17 695 122 564 1.1 1 15 549 123 567 1.1 1 23 544 124 535 1.1 1 24 511 125 524 1.1 1 24 500 126 483 1.1 1 13 470 127 445 1.1 1 19 426 128 461 1.1 1 9 452 129 367 1.1 1 17 350 130 347 1.1 1 12 335 131 353 1.1 1 24 329 132 397 1.1 1 15 382 133 389 1.1 1 13 376 134 333 1.1 1 21 312 135 333 1.1 1 12 321 136 373 1.1 1 9 364 137 355 1.1 1 6 349 138 476 1.1 1 3 473 139 481 1.1 1 3 478 140 496 1.1 1 3 493 141 701 1.1 1 4 697 142 825 1.1 1 2 823 143 1077 1.1 1 2 1075 144 1375 1.1 1 0 1375 145 1897 1.1 1 1 1896 146 2675 1.1 1 3 2672 147 4690 1.1 1 2 4688 148 9330 1.1 1 1 9329 149 17972 1.1 1 2 17970 150 100369 1.1 1 1 100368 151 23154 1.1 1 0 23154 RUN STATISTICS FOR INPUT FILE: larvae_2.fastq.gz ============================================= 72973389 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 72973389 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 919548 (1.26%)