SUMMARISING RUN PARAMETERS ========================== Input filename: DE-3_trimmed_1.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: 2438). Second best hit was smallRNA (count: 8) 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-3_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 337.774 s (4.063 µs/read; 14.77 M reads/minute). === Summary === Total reads processed: 83,123,897 Reads with adapters: 15,807,845 (19.0%) Reads written (passing filters): 83,123,897 (100.0%) Total basepairs processed: 11,500,421,315 bp Quality-trimmed: 73,878,955 bp (0.6%) Total written (filtered): 11,333,204,757 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15807845 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 34.4% G: 18.4% T: 13.1% none/other: 2.3% Overview of removed sequences length count expect max.err error counts 1 9724942 20780974.2 0 9724942 2 4281454 5195243.6 0 4281454 3 740576 1298810.9 0 740576 4 105527 324702.7 0 105527 5 44538 81175.7 0 44538 6 7495 20293.9 0 7495 7 3243 5073.5 0 3243 8 286 1268.4 0 286 9 7210 317.1 0 2720 4490 10 1285 79.3 1 275 1010 11 5423 19.8 1 455 4968 12 10582 5.0 1 167 10415 13 1656 1.2 1 509 1147 14 15736 1.2 1 449 15287 15 3382 1.2 1 651 2731 16 11615 1.2 1 1165 10450 17 10978 1.2 1 1445 9533 18 9207 1.2 1 1437 7770 19 11499 1.2 1 2179 9320 20 11369 1.2 1 2286 9083 21 17190 1.2 1 4059 13131 22 10891 1.2 1 2706 8185 23 6761 1.2 1 2013 4748 24 11422 1.2 1 3501 7921 25 9475 1.2 1 2968 6507 26 12444 1.2 1 4407 8037 27 28727 1.2 1 10397 18330 28 8144 1.2 1 2435 5709 29 9468 1.2 1 3556 5912 30 8750 1.2 1 3557 5193 31 19183 1.2 1 8896 10287 32 6152 1.2 1 2102 4050 33 15939 1.2 1 7255 8684 34 11474 1.2 1 4918 6556 35 15076 1.2 1 6383 8693 36 11354 1.2 1 5152 6202 37 13180 1.2 1 5683 7497 38 18123 1.2 1 8281 9842 39 4975 1.2 1 1812 3163 40 13319 1.2 1 6145 7174 41 14643 1.2 1 6826 7817 42 5518 1.2 1 2023 3495 43 16499 1.2 1 7426 9073 44 4928 1.2 1 2112 2816 45 9829 1.2 1 4783 5046 46 8052 1.2 1 3782 4270 47 8132 1.2 1 3901 4231 48 8833 1.2 1 4253 4580 49 8846 1.2 1 4179 4667 50 8662 1.2 1 4280 4382 51 8949 1.2 1 4224 4725 52 9127 1.2 1 4370 4757 53 8444 1.2 1 4011 4433 54 8754 1.2 1 4176 4578 55 9703 1.2 1 4656 5047 56 9284 1.2 1 4345 4939 57 7640 1.2 1 3531 4109 58 5151 1.2 1 2357 2794 59 3181 1.2 1 1487 1694 60 1793 1.2 1 804 989 61 1376 1.2 1 615 761 62 1206 1.2 1 500 706 63 1121 1.2 1 472 649 64 861 1.2 1 363 498 65 750 1.2 1 340 410 66 1024 1.2 1 466 558 67 1354 1.2 1 626 728 68 1758 1.2 1 781 977 69 1667 1.2 1 751 916 70 1598 1.2 1 691 907 71 1532 1.2 1 722 810 72 1391 1.2 1 638 753 73 1368 1.2 1 599 769 74 1246 1.2 1 549 697 75 1105 1.2 1 498 607 76 1122 1.2 1 494 628 77 922 1.2 1 392 530 78 975 1.2 1 407 568 79 896 1.2 1 386 510 80 789 1.2 1 289 500 81 847 1.2 1 313 534 82 676 1.2 1 236 440 83 689 1.2 1 256 433 84 585 1.2 1 220 365 85 539 1.2 1 206 333 86 530 1.2 1 184 346 87 478 1.2 1 163 315 88 431 1.2 1 155 276 89 422 1.2 1 168 254 90 386 1.2 1 215 171 91 385 1.2 1 216 169 92 321 1.2 1 178 143 93 313 1.2 1 173 140 94 260 1.2 1 134 126 95 261 1.2 1 119 142 96 207 1.2 1 97 110 97 247 1.2 1 122 125 98 221 1.2 1 97 124 99 208 1.2 1 99 109 100 187 1.2 1 79 108 101 125 1.2 1 49 76 102 194 1.2 1 70 124 103 171 1.2 1 76 95 104 144 1.2 1 55 89 105 105 1.2 1 46 59 106 105 1.2 1 24 81 107 94 1.2 1 9 85 108 101 1.2 1 14 87 109 82 1.2 1 17 65 110 54 1.2 1 17 37 111 95 1.2 1 17 78 112 57 1.2 1 11 46 113 67 1.2 1 15 52 114 62 1.2 1 8 54 115 62 1.2 1 10 52 116 87 1.2 1 16 71 117 80 1.2 1 16 64 118 83 1.2 1 10 73 119 68 1.2 1 14 54 120 75 1.2 1 20 55 121 58 1.2 1 15 43 122 46 1.2 1 15 31 123 59 1.2 1 6 53 124 65 1.2 1 10 55 125 71 1.2 1 15 56 126 56 1.2 1 11 45 127 71 1.2 1 20 51 128 92 1.2 1 23 69 129 99 1.2 1 19 80 130 82 1.2 1 27 55 131 90 1.2 1 19 71 132 123 1.2 1 35 88 133 113 1.2 1 49 64 134 105 1.2 1 42 63 135 133 1.2 1 35 98 136 136 1.2 1 49 87 137 134 1.2 1 38 96 138 163 1.2 1 52 111 139 151 1.2 1 50 101 140 172 1.2 1 60 112 141 319 1.2 1 120 199 142 162 1.2 1 52 110 143 179 1.2 1 66 113 144 250 1.2 1 93 157 145 272 1.2 1 92 180 146 336 1.2 1 124 212 147 493 1.2 1 150 343 148 288 1.2 1 45 243 149 4099 1.2 1 1 4098 150 339245 1.2 1 21 339224 RUN STATISTICS FOR INPUT FILE: DE-3_trimmed_1.fastq.gz ============================================= 83123897 sequences processed in total