SUMMARISING RUN PARAMETERS ========================== Input filename: DE-4_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: 2611). Second best hit was smallRNA (count: 11) 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-4_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 425.085 s (4.421 µs/read; 13.57 M reads/minute). === Summary === Total reads processed: 96,145,572 Reads with adapters: 18,454,661 (19.2%) Reads written (passing filters): 96,145,572 (100.0%) Total basepairs processed: 13,263,584,544 bp Quality-trimmed: 86,807,234 bp (0.7%) Total written (filtered): 13,081,318,571 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18454661 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.9% C: 34.9% G: 18.1% T: 13.1% none/other: 2.0% Overview of removed sequences length count expect max.err error counts 1 11395065 24036393.0 0 11395065 2 5193729 6009098.2 0 5193729 3 862858 1502274.6 0 862858 4 124407 375568.6 0 124407 5 53312 93892.2 0 53312 6 8370 23473.0 0 8370 7 2952 5868.3 0 2952 8 341 1467.1 0 341 9 4887 366.8 0 2264 2623 10 1508 91.7 1 279 1229 11 4802 22.9 1 422 4380 12 4811 5.7 1 195 4616 13 1593 1.4 1 513 1080 14 7751 1.4 1 476 7275 15 3263 1.4 1 600 2663 16 6350 1.4 1 1035 5315 17 8585 1.4 1 1699 6886 18 5660 1.4 1 1602 4058 19 8256 1.4 1 2561 5695 20 7727 1.4 1 2620 5107 21 11878 1.4 1 5211 6667 22 7425 1.4 1 3184 4241 23 4856 1.4 1 1624 3232 24 8695 1.4 1 4443 4252 25 8598 1.4 1 4442 4156 26 10532 1.4 1 5971 4561 27 26383 1.4 1 15764 10619 28 8540 1.4 1 2391 6149 29 6867 1.4 1 2869 3998 30 8262 1.4 1 5584 2678 31 18990 1.4 1 13431 5559 32 5888 1.4 1 1997 3891 33 21879 1.4 1 14630 7249 34 3975 1.4 1 1290 2685 35 12301 1.4 1 7816 4485 36 9938 1.4 1 6692 3246 37 31859 1.4 1 22501 9358 38 4707 1.4 1 1529 3178 39 9387 1.4 1 4192 5195 40 7441 1.4 1 5241 2200 41 8680 1.4 1 5417 3263 42 5124 1.4 1 2076 3048 43 11377 1.4 1 7345 4032 44 5683 1.4 1 3894 1789 45 7613 1.4 1 4868 2745 46 7548 1.4 1 5147 2401 47 7402 1.4 1 4964 2438 48 8249 1.4 1 5449 2800 49 7848 1.4 1 5049 2799 50 7539 1.4 1 4879 2660 51 7262 1.4 1 4636 2626 52 7018 1.4 1 4616 2402 53 6941 1.4 1 4503 2438 54 6603 1.4 1 4267 2336 55 6935 1.4 1 4506 2429 56 7260 1.4 1 4791 2469 57 6958 1.4 1 4568 2390 58 5383 1.4 1 3489 1894 59 3830 1.4 1 2430 1400 60 2369 1.4 1 1450 919 61 1610 1.4 1 1020 590 62 1235 1.4 1 794 441 63 1060 1.4 1 656 404 64 765 1.4 1 455 310 65 659 1.4 1 414 245 66 751 1.4 1 531 220 67 902 1.4 1 564 338 68 1070 1.4 1 721 349 69 1072 1.4 1 747 325 70 1101 1.4 1 728 373 71 1075 1.4 1 679 396 72 1006 1.4 1 649 357 73 936 1.4 1 612 324 74 897 1.4 1 551 346 75 850 1.4 1 527 323 76 756 1.4 1 484 272 77 682 1.4 1 396 286 78 666 1.4 1 418 248 79 604 1.4 1 313 291 80 623 1.4 1 295 328 81 607 1.4 1 242 365 82 557 1.4 1 280 277 83 471 1.4 1 206 265 84 467 1.4 1 228 239 85 446 1.4 1 187 259 86 409 1.4 1 185 224 87 352 1.4 1 162 190 88 379 1.4 1 139 240 89 380 1.4 1 166 214 90 342 1.4 1 242 100 91 297 1.4 1 193 104 92 309 1.4 1 188 121 93 255 1.4 1 153 102 94 245 1.4 1 160 85 95 207 1.4 1 127 80 96 266 1.4 1 156 110 97 220 1.4 1 137 83 98 199 1.4 1 119 80 99 203 1.4 1 106 97 100 187 1.4 1 96 91 101 143 1.4 1 80 63 102 185 1.4 1 88 97 103 133 1.4 1 80 53 104 127 1.4 1 55 72 105 135 1.4 1 50 85 106 77 1.4 1 22 55 107 93 1.4 1 36 57 108 68 1.4 1 22 46 109 80 1.4 1 18 62 110 62 1.4 1 19 43 111 74 1.4 1 18 56 112 63 1.4 1 20 43 113 68 1.4 1 18 50 114 61 1.4 1 8 53 115 65 1.4 1 25 40 116 88 1.4 1 10 78 117 61 1.4 1 9 52 118 86 1.4 1 9 77 119 87 1.4 1 15 72 120 52 1.4 1 9 43 121 80 1.4 1 16 64 122 64 1.4 1 15 49 123 48 1.4 1 7 41 124 49 1.4 1 15 34 125 74 1.4 1 21 53 126 71 1.4 1 21 50 127 64 1.4 1 20 44 128 67 1.4 1 18 49 129 81 1.4 1 18 63 130 49 1.4 1 14 35 131 75 1.4 1 26 49 132 88 1.4 1 38 50 133 119 1.4 1 44 75 134 123 1.4 1 61 62 135 160 1.4 1 70 90 136 122 1.4 1 54 68 137 128 1.4 1 61 67 138 163 1.4 1 90 73 139 131 1.4 1 69 62 140 199 1.4 1 106 93 141 255 1.4 1 133 122 142 146 1.4 1 67 79 143 177 1.4 1 105 72 144 189 1.4 1 82 107 145 233 1.4 1 121 112 146 313 1.4 1 178 135 147 533 1.4 1 227 306 148 252 1.4 1 57 195 149 4197 1.4 1 2 4195 150 347235 1.4 1 11 347224 RUN STATISTICS FOR INPUT FILE: DE-4_trimmed_1.fastq.gz ============================================= 96145572 sequences processed in total