SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245602_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 52392). Second best hit was smallRNA (count: 0) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 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 Output file will be GZIP compressed This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245602_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3976.466 s (50.103 µs/read; 1.20 M reads/minute). === Summary === Total reads processed: 79,365,519 Reads with adapters: 43,173,753 (54.4%) Reads written (passing filters): 79,365,519 (100.0%) Total basepairs processed: 11,904,827,850 bp Quality-trimmed: 34,066,459 bp (0.3%) Total written (filtered): 11,628,791,406 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43173753 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.6% C: 19.5% G: 0.4% T: 31.3% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 37048372 19841379.8 0 37048372 2 214067 4960344.9 0 214067 3 225981 1240086.2 0 225981 4 212068 310021.6 0 212068 5 176853 77505.4 0 176853 6 160644 19376.3 0 160644 7 165342 4844.1 0 165342 8 173482 1211.0 0 173482 9 139080 302.8 0 138542 538 10 154291 75.7 1 145727 8564 11 149485 18.9 1 138719 10766 12 152392 4.7 1 142108 10284 13 131245 1.2 1 123047 8198 14 140800 1.2 1 131137 9663 15 127226 1.2 1 118890 8336 16 123382 1.2 1 115575 7807 17 133892 1.2 1 125660 8232 18 100798 1.2 1 94583 6215 19 121957 1.2 1 114431 7526 20 115038 1.2 1 108150 6888 21 93040 1.2 1 86651 6389 22 97737 1.2 1 92196 5541 23 95550 1.2 1 90030 5520 24 109384 1.2 1 102370 7014 25 97996 1.2 1 92619 5377 26 75017 1.2 1 70424 4593 27 75240 1.2 1 69871 5369 28 80573 1.2 1 76603 3970 29 73773 1.2 1 69146 4627 30 74548 1.2 1 70802 3746 31 67859 1.2 1 63953 3906 32 66774 1.2 1 63359 3415 33 74783 1.2 1 70532 4251 34 63309 1.2 1 59068 4241 35 55338 1.2 1 52488 2850 36 61283 1.2 1 58486 2797 37 57656 1.2 1 54668 2988 38 50365 1.2 1 47964 2401 39 53328 1.2 1 50830 2498 40 45794 1.2 1 43546 2248 41 46899 1.2 1 44666 2233 42 60542 1.2 1 57891 2651 43 35328 1.2 1 33025 2303 44 66228 1.2 1 63356 2872 45 56756 1.2 1 54101 2655 46 34457 1.2 1 31941 2516 47 73928 1.2 1 72160 1768 48 13220 1.2 1 11954 1266 49 40292 1.2 1 38706 1586 50 11307 1.2 1 10494 813 51 23960 1.2 1 22873 1087 52 12909 1.2 1 12071 838 53 29730 1.2 1 28351 1379 54 46488 1.2 1 45113 1375 55 13449 1.2 1 12452 997 56 30449 1.2 1 28300 2149 57 110530 1.2 1 108273 2257 58 17656 1.2 1 16565 1091 59 9383 1.2 1 8390 993 60 57102 1.2 1 55647 1455 61 10994 1.2 1 10369 625 62 9446 1.2 1 8501 945 63 53084 1.2 1 51382 1702 64 49781 1.2 1 48583 1198 65 5983 1.2 1 5422 561 66 13590 1.2 1 13035 555 67 8122 1.2 1 7806 316 68 6824 1.2 1 6390 434 69 9392 1.2 1 8961 431 70 16354 1.2 1 15915 439 71 7082 1.2 1 6776 306 72 7124 1.2 1 6774 350 73 9473 1.2 1 9097 376 74 10073 1.2 1 9570 503 75 14716 1.2 1 14156 560 76 15831 1.2 1 15226 605 77 10995 1.2 1 10509 486 78 12050 1.2 1 11531 519 79 12057 1.2 1 11564 493 80 12601 1.2 1 12114 487 81 12603 1.2 1 12052 551 82 13276 1.2 1 12746 530 83 15654 1.2 1 15006 648 84 14824 1.2 1 14168 656 85 15816 1.2 1 15200 616 86 12899 1.2 1 12362 537 87 12064 1.2 1 11590 474 88 11590 1.2 1 11138 452 89 11196 1.2 1 10784 412 90 11627 1.2 1 11237 390 91 10650 1.2 1 10278 372 92 10810 1.2 1 10412 398 93 10645 1.2 1 10255 390 94 10182 1.2 1 9781 401 95 10192 1.2 1 9831 361 96 10013 1.2 1 9620 393 97 9890 1.2 1 9502 388 98 10871 1.2 1 10466 405 99 10898 1.2 1 10571 327 100 11176 1.2 1 10824 352 101 9916 1.2 1 9567 349 102 9286 1.2 1 8982 304 103 9003 1.2 1 8687 316 104 8846 1.2 1 8515 331 105 9044 1.2 1 8707 337 106 8891 1.2 1 8552 339 107 8955 1.2 1 8650 305 108 8988 1.2 1 8647 341 109 8652 1.2 1 8383 269 110 8556 1.2 1 8247 309 111 8744 1.2 1 8468 276 112 8465 1.2 1 8149 316 113 8334 1.2 1 8029 305 114 8538 1.2 1 8253 285 115 8622 1.2 1 8293 329 116 8908 1.2 1 8619 289 117 8659 1.2 1 8337 322 118 8542 1.2 1 8249 293 119 8668 1.2 1 8342 326 120 8533 1.2 1 8151 382 121 8498 1.2 1 8031 467 122 8388 1.2 1 7804 584 123 9002 1.2 1 8253 749 124 8656 1.2 1 7801 855 125 8619 1.2 1 7591 1028 126 8564 1.2 1 7263 1301 127 8107 1.2 1 6605 1502 128 8147 1.2 1 6471 1676 129 8478 1.2 1 6597 1881 130 7982 1.2 1 5747 2235 131 7992 1.2 1 5408 2584 132 8200 1.2 1 5114 3086 133 8323 1.2 1 4835 3488 134 7891 1.2 1 4329 3562 135 7190 1.2 1 3741 3449 136 6565 1.2 1 3257 3308 137 5491 1.2 1 3065 2426 138 4984 1.2 1 3378 1606 139 4463 1.2 1 3248 1215 140 4136 1.2 1 3162 974 141 4610 1.2 1 3928 682 142 3723 1.2 1 3170 553 143 3774 1.2 1 3226 548 144 4863 1.2 1 4170 693 145 5982 1.2 1 5050 932 146 3389 1.2 1 2692 697 147 652 1.2 1 456 196 148 5363 1.2 1 4444 919 149 2328 1.2 1 1825 503 150 54440 1.2 1 47199 7241 RUN STATISTICS FOR INPUT FILE: SRR18245602_2.fastq.gz ============================================= 79365519 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 79365519 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 183598 (0.23%)