SUMMARISING RUN PARAMETERS ========================== Input filename: DE-2_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: 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_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 349.930 s (4.108 µs/read; 14.61 M reads/minute). === Summary === Total reads processed: 85,186,843 Reads with adapters: 15,924,182 (18.7%) Reads written (passing filters): 85,186,843 (100.0%) Total basepairs processed: 11,918,707,569 bp Quality-trimmed: 75,010,722 bp (0.6%) Total written (filtered): 11,741,544,923 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15924182 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.1% C: 33.5% G: 18.3% T: 13.4% none/other: 2.7% Overview of removed sequences length count expect max.err error counts 1 9981055 21296710.8 0 9981055 2 4078374 5324177.7 0 4078374 3 770132 1331044.4 0 770132 4 109485 332761.1 0 109485 5 44223 83190.3 0 44223 6 7269 20797.6 0 7269 7 3126 5199.4 0 3126 8 270 1299.8 0 270 9 5856 325.0 0 2184 3672 10 1260 81.2 1 266 994 11 4841 20.3 1 359 4482 12 8727 5.1 1 141 8586 13 1566 1.3 1 479 1087 14 13122 1.3 1 575 12547 15 3089 1.3 1 545 2544 16 9999 1.3 1 1429 8570 17 9484 1.3 1 1577 7907 18 8511 1.3 1 1969 6542 19 10734 1.3 1 2700 8034 20 10376 1.3 1 2929 7447 21 16343 1.3 1 5534 10809 22 10144 1.3 1 3615 6529 23 6205 1.3 1 2165 4040 24 11281 1.3 1 4833 6448 25 9499 1.3 1 4175 5324 26 12754 1.3 1 6024 6730 27 29346 1.3 1 14371 14975 28 7828 1.3 1 2374 5454 29 8933 1.3 1 3794 5139 30 9962 1.3 1 5475 4487 31 19876 1.3 1 11792 8084 32 5124 1.3 1 2140 2984 33 15635 1.3 1 8771 6864 34 10823 1.3 1 5904 4919 35 12263 1.3 1 6956 5307 36 13175 1.3 1 7210 5965 37 13807 1.3 1 7200 6607 38 33136 1.3 1 19427 13709 39 6022 1.3 1 2070 3952 40 10169 1.3 1 4986 5183 41 7553 1.3 1 4395 3158 42 2250 1.3 1 907 1343 43 12018 1.3 1 6892 5126 44 5425 1.3 1 3146 2279 45 8354 1.3 1 4895 3459 46 7724 1.3 1 4602 3122 47 7563 1.3 1 4388 3175 48 8061 1.3 1 4612 3449 49 7923 1.3 1 4523 3400 50 7366 1.3 1 4182 3184 51 7364 1.3 1 4212 3152 52 7222 1.3 1 4165 3057 53 7048 1.3 1 4026 3022 54 6987 1.3 1 4021 2966 55 7590 1.3 1 4523 3067 56 7715 1.3 1 4571 3144 57 6874 1.3 1 3970 2904 58 5055 1.3 1 2897 2158 59 3436 1.3 1 1887 1549 60 2108 1.3 1 1130 978 61 1491 1.3 1 824 667 62 1151 1.3 1 635 516 63 897 1.3 1 489 408 64 752 1.3 1 409 343 65 682 1.3 1 365 317 66 769 1.3 1 421 348 67 931 1.3 1 521 410 68 1071 1.3 1 590 481 69 1153 1.3 1 664 489 70 1180 1.3 1 700 480 71 1058 1.3 1 611 447 72 1065 1.3 1 586 479 73 955 1.3 1 550 405 74 888 1.3 1 494 394 75 813 1.3 1 443 370 76 773 1.3 1 404 369 77 654 1.3 1 341 313 78 663 1.3 1 327 336 79 585 1.3 1 306 279 80 591 1.3 1 269 322 81 572 1.3 1 243 329 82 492 1.3 1 202 290 83 467 1.3 1 192 275 84 406 1.3 1 185 221 85 404 1.3 1 164 240 86 363 1.3 1 160 203 87 336 1.3 1 145 191 88 346 1.3 1 135 211 89 304 1.3 1 147 157 90 285 1.3 1 167 118 91 296 1.3 1 159 137 92 241 1.3 1 129 112 93 231 1.3 1 144 87 94 217 1.3 1 112 105 95 218 1.3 1 134 84 96 226 1.3 1 123 103 97 193 1.3 1 89 104 98 136 1.3 1 71 65 99 185 1.3 1 106 79 100 123 1.3 1 51 72 101 142 1.3 1 65 77 102 147 1.3 1 64 83 103 111 1.3 1 46 65 104 126 1.3 1 40 86 105 104 1.3 1 24 80 106 88 1.3 1 26 62 107 82 1.3 1 28 54 108 67 1.3 1 12 55 109 79 1.3 1 25 54 110 62 1.3 1 22 40 111 73 1.3 1 23 50 112 56 1.3 1 19 37 113 52 1.3 1 16 36 114 52 1.3 1 10 42 115 52 1.3 1 10 42 116 70 1.3 1 2 68 117 80 1.3 1 15 65 118 86 1.3 1 13 73 119 64 1.3 1 7 57 120 62 1.3 1 4 58 121 80 1.3 1 10 70 122 66 1.3 1 14 52 123 57 1.3 1 7 50 124 44 1.3 1 8 36 125 58 1.3 1 19 39 126 58 1.3 1 7 51 127 63 1.3 1 16 47 128 75 1.3 1 12 63 129 76 1.3 1 18 58 130 65 1.3 1 12 53 131 78 1.3 1 24 54 132 72 1.3 1 22 50 133 108 1.3 1 55 53 134 111 1.3 1 38 73 135 109 1.3 1 32 77 136 110 1.3 1 42 68 137 131 1.3 1 59 72 138 130 1.3 1 68 62 139 137 1.3 1 54 83 140 166 1.3 1 64 102 141 250 1.3 1 120 130 142 169 1.3 1 55 114 143 180 1.3 1 75 105 144 199 1.3 1 79 120 145 260 1.3 1 96 164 146 369 1.3 1 158 211 147 493 1.3 1 181 312 148 312 1.3 1 55 257 149 4398 1.3 1 2 4396 150 410480 1.3 1 15 410465 RUN STATISTICS FOR INPUT FILE: DE-2_trimmed_1.fastq.gz ============================================= 85186843 sequences processed in total