SUMMARISING RUN PARAMETERS ========================== Input filename: DE-2_trimmed_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.9 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 2810). Second best hit was Nextera (count: 24) 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: -t 12 Output file will be GZIP compressed This is cutadapt 4.9 with Python 3.12.8 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC DE-2_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 359.068 s (4.215 µs/read; 14.23 M reads/minute). === Summary === Total reads processed: 85,186,843 Reads with adapters: 21,127,800 (24.8%) Reads written (passing filters): 85,186,843 (100.0%) Total basepairs processed: 12,179,659,374 bp Quality-trimmed: 141,671,476 bp (1.2%) Total written (filtered): 11,790,811,263 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21127800 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.0% C: 33.8% G: 28.4% T: 11.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9250914 21296710.8 0 9250914 2 4206567 5324177.7 0 4206567 3 844221 1331044.4 0 844221 4 98178 332761.1 0 98178 5 33745 83190.3 0 33745 6 8460 20797.6 0 8460 7 4780 5199.4 0 4780 8 2343 1299.8 0 2343 9 12457 325.0 0 8646 3811 10 7356 81.2 1 3808 3548 11 11933 20.3 1 5393 6540 12 17266 5.1 1 9029 8237 13 8243 1.3 1 2932 5311 14 13623 1.3 1 5707 7916 15 18857 1.3 1 8675 10182 16 17561 1.3 1 8099 9462 17 27368 1.3 1 16007 11361 18 34934 1.3 1 18572 16362 19 134339 1.3 1 101315 33024 20 49890 1.3 1 36811 13079 21 21169 1.3 1 11717 9452 22 26104 1.3 1 13456 12648 23 45787 1.3 1 25084 20703 24 528475 1.3 1 472550 55925 25 195478 1.3 1 166262 29216 26 223854 1.3 1 196857 26997 27 1256381 1.3 1 1202925 53456 28 153838 1.3 1 137319 16519 29 470203 1.3 1 449822 20381 30 94245 1.3 1 86885 7360 31 63845 1.3 1 56129 7716 32 306446 1.3 1 289942 16504 33 124679 1.3 1 109409 15270 34 754997 1.3 1 725237 29760 35 163022 1.3 1 148116 14906 36 458231 1.3 1 436145 22086 37 53521 1.3 1 46797 6724 38 91031 1.3 1 85987 5044 39 26235 1.3 1 22540 3695 40 100781 1.3 1 91553 9228 41 219082 1.3 1 206284 12798 42 38570 1.3 1 33441 5129 43 42486 1.3 1 37707 4779 44 35667 1.3 1 29231 6436 45 114686 1.3 1 106778 7908 46 33590 1.3 1 30199 3391 47 25128 1.3 1 22313 2815 48 5271 1.3 1 4210 1061 49 21884 1.3 1 19652 2232 50 65500 1.3 1 61846 3654 51 17434 1.3 1 14776 2658 52 37454 1.3 1 34915 2539 53 31042 1.3 1 28435 2607 54 14643 1.3 1 12735 1908 55 43467 1.3 1 41192 2275 56 14169 1.3 1 12543 1626 57 17400 1.3 1 15900 1500 58 17687 1.3 1 16128 1559 59 37020 1.3 1 34458 2562 60 20015 1.3 1 18291 1724 61 14868 1.3 1 13253 1615 62 29913 1.3 1 28304 1609 63 9315 1.3 1 8096 1219 64 18259 1.3 1 17127 1132 65 9621 1.3 1 8626 995 66 10651 1.3 1 9605 1046 67 12534 1.3 1 11545 989 68 19583 1.3 1 18410 1173 69 15014 1.3 1 13979 1035 70 9444 1.3 1 8622 822 71 16427 1.3 1 15615 812 72 8986 1.3 1 8278 708 73 9209 1.3 1 8642 567 74 10722 1.3 1 10142 580 75 10292 1.3 1 9850 442 76 3985 1.3 1 3669 316 77 1132 1.3 1 933 199 78 1466 1.3 1 1268 198 79 2692 1.3 1 2441 251 80 3523 1.3 1 3234 289 81 3807 1.3 1 3573 234 82 3791 1.3 1 3488 303 83 3507 1.3 1 3228 279 84 3329 1.3 1 3062 267 85 3125 1.3 1 2848 277 86 2766 1.3 1 2505 261 87 2601 1.3 1 2386 215 88 2441 1.3 1 2244 197 89 2246 1.3 1 2062 184 90 2189 1.3 1 1979 210 91 2004 1.3 1 1797 207 92 1890 1.3 1 1715 175 93 1791 1.3 1 1576 215 94 1757 1.3 1 1514 243 95 1533 1.3 1 1384 149 96 1455 1.3 1 1336 119 97 1478 1.3 1 1295 183 98 1227 1.3 1 1130 97 99 1222 1.3 1 1070 152 100 1164 1.3 1 1030 134 101 1115 1.3 1 958 157 102 1169 1.3 1 929 240 103 921 1.3 1 807 114 104 934 1.3 1 797 137 105 892 1.3 1 763 129 106 795 1.3 1 685 110 107 792 1.3 1 656 136 108 724 1.3 1 577 147 109 681 1.3 1 532 149 110 667 1.3 1 556 111 111 581 1.3 1 483 98 112 645 1.3 1 482 163 113 590 1.3 1 457 133 114 495 1.3 1 417 78 115 485 1.3 1 397 88 116 435 1.3 1 358 77 117 477 1.3 1 368 109 118 556 1.3 1 348 208 119 391 1.3 1 324 67 120 390 1.3 1 299 91 121 407 1.3 1 317 90 122 422 1.3 1 303 119 123 403 1.3 1 295 108 124 330 1.3 1 269 61 125 393 1.3 1 307 86 126 499 1.3 1 363 136 127 449 1.3 1 363 86 128 540 1.3 1 451 89 129 651 1.3 1 504 147 130 556 1.3 1 494 62 131 699 1.3 1 586 113 132 726 1.3 1 620 106 133 870 1.3 1 757 113 134 1099 1.3 1 996 103 135 1064 1.3 1 935 129 136 1178 1.3 1 1045 133 137 1454 1.3 1 1318 136 138 1520 1.3 1 1399 121 139 1435 1.3 1 1322 113 140 1739 1.3 1 1591 148 141 2576 1.3 1 2370 206 142 1472 1.3 1 1295 177 143 1676 1.3 1 1531 145 144 2108 1.3 1 1951 157 145 2350 1.3 1 2216 134 146 3781 1.3 1 3571 210 147 4746 1.3 1 4408 338 148 1355 1.3 1 1210 145 149 247 1.3 1 96 151 150 809 1.3 1 476 333 RUN STATISTICS FOR INPUT FILE: DE-2_trimmed_2.fastq.gz ============================================= 85186843 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 85186843 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 707739 (0.83%)