SUMMARISING RUN PARAMETERS ========================== Input filename: DE-5_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: 2826). Second best hit was Nextera (count: 12) 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-5_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 351.052 s (4.289 µs/read; 13.99 M reads/minute). === Summary === Total reads processed: 81,854,062 Reads with adapters: 15,731,737 (19.2%) Reads written (passing filters): 81,854,062 (100.0%) Total basepairs processed: 11,272,115,580 bp Quality-trimmed: 77,961,197 bp (0.7%) Total written (filtered): 11,072,630,461 bp (98.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15731737 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.4% C: 35.1% G: 16.6% T: 12.2% none/other: 3.6% Overview of removed sequences length count expect max.err error counts 1 9724176 20463515.5 0 9724176 2 4195074 5115878.9 0 4195074 3 662762 1278969.7 0 662762 4 90895 319742.4 0 90895 5 41391 79935.6 0 41391 6 6094 19983.9 0 6094 7 2585 4996.0 0 2585 8 294 1249.0 0 294 9 4239 312.2 0 1949 2290 10 1252 78.1 1 285 967 11 4405 19.5 1 377 4028 12 5447 4.9 1 193 5254 13 1422 1.2 1 454 968 14 8507 1.2 1 530 7977 15 3134 1.2 1 560 2574 16 6843 1.2 1 1132 5711 17 8171 1.2 1 1647 6524 18 6178 1.2 1 1793 4385 19 8247 1.2 1 2566 5681 20 8058 1.2 1 2767 5291 21 12638 1.2 1 5398 7240 22 7868 1.2 1 3265 4603 23 4744 1.2 1 1625 3119 24 9149 1.2 1 4533 4616 25 8338 1.2 1 4103 4235 26 10514 1.2 1 5713 4801 27 25490 1.2 1 14783 10707 28 7347 1.2 1 2158 5189 29 7127 1.2 1 3069 4058 30 8392 1.2 1 5358 3034 31 18813 1.2 1 12723 6090 32 5198 1.2 1 1953 3245 33 14386 1.2 1 8743 5643 34 18849 1.2 1 11937 6912 35 10674 1.2 1 6623 4051 36 6415 1.2 1 2787 3628 37 9716 1.2 1 6004 3712 38 8595 1.2 1 5790 2805 39 10692 1.2 1 6333 4359 40 10371 1.2 1 6382 3989 41 15293 1.2 1 10010 5283 42 4789 1.2 1 1848 2941 43 13998 1.2 1 8620 5378 44 4927 1.2 1 2871 2056 45 8233 1.2 1 5072 3161 46 7332 1.2 1 4644 2688 47 7242 1.2 1 4729 2513 48 7686 1.2 1 4886 2800 49 7616 1.2 1 4795 2821 50 7364 1.2 1 4591 2773 51 7742 1.2 1 4861 2881 52 7868 1.2 1 5067 2801 53 6526 1.2 1 4048 2478 54 6958 1.2 1 4565 2393 55 7698 1.2 1 5085 2613 56 6860 1.2 1 4438 2422 57 5074 1.2 1 3154 1920 58 3132 1.2 1 1887 1245 59 1971 1.2 1 1149 822 60 1169 1.2 1 607 562 61 1056 1.2 1 636 420 62 930 1.2 1 584 346 63 770 1.2 1 452 318 64 577 1.2 1 326 251 65 647 1.2 1 393 254 66 774 1.2 1 512 262 67 989 1.2 1 621 368 68 1142 1.2 1 696 446 69 1175 1.2 1 753 422 70 1026 1.2 1 645 381 71 956 1.2 1 590 366 72 858 1.2 1 531 327 73 824 1.2 1 463 361 74 798 1.2 1 468 330 75 696 1.2 1 437 259 76 694 1.2 1 379 315 77 653 1.2 1 353 300 78 594 1.2 1 327 267 79 534 1.2 1 275 259 80 523 1.2 1 250 273 81 533 1.2 1 239 294 82 462 1.2 1 234 228 83 432 1.2 1 189 243 84 397 1.2 1 173 224 85 358 1.2 1 163 195 86 352 1.2 1 159 193 87 310 1.2 1 121 189 88 316 1.2 1 124 192 89 324 1.2 1 169 155 90 273 1.2 1 177 96 91 257 1.2 1 173 84 92 253 1.2 1 172 81 93 227 1.2 1 144 83 94 206 1.2 1 133 73 95 180 1.2 1 115 65 96 174 1.2 1 110 64 97 189 1.2 1 113 76 98 196 1.2 1 110 86 99 156 1.2 1 84 72 100 146 1.2 1 84 62 101 113 1.2 1 66 47 102 155 1.2 1 79 76 103 110 1.2 1 61 49 104 111 1.2 1 59 52 105 101 1.2 1 50 51 106 93 1.2 1 39 54 107 78 1.2 1 16 62 108 82 1.2 1 24 58 109 80 1.2 1 28 52 110 66 1.2 1 25 41 111 66 1.2 1 17 49 112 56 1.2 1 11 45 113 55 1.2 1 18 37 114 52 1.2 1 16 36 115 72 1.2 1 14 58 116 73 1.2 1 14 59 117 59 1.2 1 13 46 118 65 1.2 1 17 48 119 74 1.2 1 14 60 120 70 1.2 1 13 57 121 73 1.2 1 16 57 122 55 1.2 1 14 41 123 93 1.2 1 30 63 124 54 1.2 1 8 46 125 72 1.2 1 26 46 126 69 1.2 1 38 31 127 76 1.2 1 18 58 128 89 1.2 1 33 56 129 97 1.2 1 30 67 130 103 1.2 1 41 62 131 108 1.2 1 38 70 132 98 1.2 1 43 55 133 134 1.2 1 45 89 134 141 1.2 1 71 70 135 164 1.2 1 77 87 136 153 1.2 1 72 81 137 201 1.2 1 101 100 138 171 1.2 1 99 72 139 162 1.2 1 84 78 140 243 1.2 1 135 108 141 402 1.2 1 213 189 142 217 1.2 1 112 105 143 227 1.2 1 120 107 144 287 1.2 1 141 146 145 312 1.2 1 166 146 146 471 1.2 1 245 226 147 641 1.2 1 303 338 148 452 1.2 1 74 378 149 6639 1.2 1 5 6634 150 552177 1.2 1 26 552151 RUN STATISTICS FOR INPUT FILE: DE-5_trimmed_1.fastq.gz ============================================= 81854062 sequences processed in total