SUMMARISING RUN PARAMETERS ========================== Input filename: larvae_1.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_1.fastq.gz Processing reads on 4 cores in single-end mode ... Finished in 761.77 s (10 µs/read; 5.75 M reads/minute). === Summary === Total reads processed: 72,973,389 Reads with adapters: 20,851,759 (28.6%) Reads written (passing filters): 72,973,389 (100.0%) Total basepairs processed: 10,589,369,419 bp Quality-trimmed: 205,686,558 bp (1.9%) Total written (filtered): 10,251,316,851 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20851759 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.5% C: 28.8% G: 14.0% T: 19.5% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 16867610 18243347.2 0 16867610 3 944521 1140209.2 0 944521 4 321214 285052.3 0 321214 5 209736 71263.1 0 209736 8 58611 1113.5 0 58611 9 94238 278.4 0 94238 10 1118 69.6 1 0 1118 11 102008 17.4 1 93079 8929 12 3171 4.3 1 0 3171 13 49695 1.1 1 44244 5451 14 54330 1.1 1 44722 9608 15 53352 1.1 1 46325 7027 16 56052 1.1 1 45794 10258 17 110528 1.1 1 97303 13225 18 6396 1.1 1 2696 3700 19 38160 1.1 1 33581 4579 20 54439 1.1 1 45460 8979 21 86389 1.1 1 79036 7353 22 8081 1.1 1 4359 3722 23 44025 1.1 1 40530 3495 24 44173 1.1 1 38381 5792 25 45225 1.1 1 39932 5293 26 41817 1.1 1 36777 5040 27 49125 1.1 1 41418 7707 28 43760 1.1 1 37562 6198 29 78477 1.1 1 71852 6625 30 3864 1.1 1 2261 1603 31 30460 1.1 1 26700 3760 32 34655 1.1 1 31470 3185 33 37998 1.1 1 32558 5440 34 59808 1.1 1 55272 4536 35 7009 1.1 1 4761 2248 36 29522 1.1 1 26762 2760 37 32193 1.1 1 28627 3566 38 32496 1.1 1 26643 5853 39 68625 1.1 1 63911 4714 40 6442 1.1 1 4695 1747 41 3073 1.1 1 1696 1377 42 26588 1.1 1 23683 2905 43 21838 1.1 1 18085 3753 44 34823 1.1 1 19096 15727 45 42574 1.1 1 37891 4683 46 60306 1.1 1 10438 49868 47 119866 1.1 1 114186 5680 48 6387 1.1 1 3851 2536 49 4763 1.1 1 3063 1700 50 29924 1.1 1 7330 22594 51 46843 1.1 1 43922 2921 52 7021 1.1 1 5611 1410 53 13469 1.1 1 3351 10118 54 15889 1.1 1 14785 1104 55 3231 1.1 1 2121 1110 56 2963 1.1 1 1822 1141 57 4091 1.1 1 3299 792 58 3497 1.1 1 1857 1640 59 4911 1.1 1 4122 789 60 2770 1.1 1 1953 817 61 1439 1.1 1 1071 368 62 2639 1.1 1 1896 743 63 2296 1.1 1 1670 626 64 2946 1.1 1 1962 984 65 1845 1.1 1 1474 371 66 2899 1.1 1 1982 917 67 3691 1.1 1 3136 555 68 3828 1.1 1 3210 618 69 4976 1.1 1 4214 762 70 4272 1.1 1 3590 682 71 1926 1.1 1 1315 611 72 1303 1.1 1 471 832 73 1532 1.1 1 331 1201 74 2806 1.1 1 314 2492 75 15323 1.1 1 462 14861 76 24270 1.1 1 473 23797 77 53434 1.1 1 463 52971 78 64322 1.1 1 427 63895 79 56864 1.1 1 314 56550 80 42601 1.1 1 188 42413 81 29709 1.1 1 125 29584 82 21089 1.1 1 81 21008 83 15239 1.1 1 52 15187 84 12091 1.1 1 35 12056 85 11531 1.1 1 54 11477 86 9448 1.1 1 33 9415 87 7786 1.1 1 30 7756 88 6564 1.1 1 27 6537 89 5827 1.1 1 31 5796 90 4608 1.1 1 25 4583 91 4016 1.1 1 20 3996 92 3448 1.1 1 19 3429 93 2787 1.1 1 14 2773 94 2246 1.1 1 15 2231 95 2064 1.1 1 14 2050 96 1675 1.1 1 11 1664 97 1510 1.1 1 12 1498 98 1500 1.1 1 15 1485 99 1331 1.1 1 11 1320 100 1163 1.1 1 7 1156 101 1012 1.1 1 10 1002 102 940 1.1 1 9 931 103 964 1.1 1 7 957 104 966 1.1 1 9 957 105 1054 1.1 1 4 1050 106 1138 1.1 1 9 1129 107 1153 1.1 1 11 1142 108 1255 1.1 1 15 1240 109 1187 1.1 1 9 1178 110 1221 1.1 1 17 1204 111 1269 1.1 1 13 1256 112 1237 1.1 1 12 1225 113 1177 1.1 1 5 1172 114 1051 1.1 1 13 1038 115 1015 1.1 1 12 1003 116 936 1.1 1 8 928 117 771 1.1 1 6 765 118 826 1.1 1 10 816 119 681 1.1 1 4 677 120 624 1.1 1 3 621 121 601 1.1 1 11 590 122 551 1.1 1 8 543 123 523 1.1 1 3 520 124 477 1.1 1 13 464 125 442 1.1 1 7 435 126 469 1.1 1 10 459 127 367 1.1 1 7 360 128 419 1.1 1 6 413 129 373 1.1 1 6 367 130 348 1.1 1 4 344 131 295 1.1 1 7 288 132 397 1.1 1 8 389 133 314 1.1 1 11 303 134 311 1.1 1 6 305 135 332 1.1 1 5 327 136 312 1.1 1 10 302 137 317 1.1 1 4 313 138 330 1.1 1 6 324 139 360 1.1 1 4 356 140 379 1.1 1 3 376 141 481 1.1 1 2 479 142 563 1.1 1 3 560 143 690 1.1 1 0 690 144 829 1.1 1 1 828 145 1225 1.1 1 1 1224 146 1755 1.1 1 1 1754 147 3494 1.1 1 4 3490 148 7692 1.1 1 3 7689 149 13064 1.1 1 1 13063 150 60370 1.1 1 1 60369 151 28208 1.1 1 1 28207 RUN STATISTICS FOR INPUT FILE: larvae_1.fastq.gz ============================================= 72973389 sequences processed in total