SUMMARISING RUN PARAMETERS ========================== Input filename: DE-3C_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: 2019). Second best hit was Nextera (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-3C_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 347.085 s (4.292 µs/read; 13.98 M reads/minute). === Summary === Total reads processed: 80,872,082 Reads with adapters: 15,218,152 (18.8%) Reads written (passing filters): 80,872,082 (100.0%) Total basepairs processed: 11,154,114,963 bp Quality-trimmed: 72,060,668 bp (0.6%) Total written (filtered): 10,983,731,438 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15218152 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 35.4% G: 18.4% T: 12.4% none/other: 2.8% Overview of removed sequences length count expect max.err error counts 1 9203034 20218020.5 0 9203034 2 4345482 5054505.1 0 4345482 3 683169 1263626.3 0 683169 4 96600 315906.6 0 96600 5 42152 78976.6 0 42152 6 6892 19744.2 0 6892 7 2997 4936.0 0 2997 8 295 1234.0 0 295 9 5484 308.5 0 2360 3124 10 1287 77.1 1 282 1005 11 4820 19.3 1 413 4407 12 7000 4.8 1 151 6849 13 1582 1.2 1 478 1104 14 10748 1.2 1 407 10341 15 2947 1.2 1 601 2346 16 8211 1.2 1 1054 7157 17 8501 1.2 1 1292 7209 18 6678 1.2 1 1247 5431 19 8548 1.2 1 1796 6752 20 8284 1.2 1 1984 6300 21 12740 1.2 1 3370 9370 22 8108 1.2 1 2363 5745 23 5563 1.2 1 1855 3708 24 8551 1.2 1 3046 5505 25 7634 1.2 1 2558 5076 26 9610 1.2 1 3853 5757 27 22043 1.2 1 9169 12874 28 8337 1.2 1 2596 5741 29 9009 1.2 1 3836 5173 30 6501 1.2 1 3119 3382 31 17106 1.2 1 8761 8345 32 14202 1.2 1 6486 7716 33 8483 1.2 1 3841 4642 34 30167 1.2 1 16335 13832 35 3376 1.2 1 956 2420 36 11918 1.2 1 5569 6349 37 642 1.2 1 224 418 38 547 1.2 1 229 318 39 6125 1.2 1 3307 2818 40 7451 1.2 1 3556 3895 41 13285 1.2 1 6794 6491 42 5763 1.2 1 2124 3639 43 12510 1.2 1 6219 6291 44 4038 1.2 1 1963 2075 45 7218 1.2 1 3814 3404 46 6326 1.2 1 3263 3063 47 5993 1.2 1 3179 2814 48 6845 1.2 1 3513 3332 49 6699 1.2 1 3472 3227 50 6371 1.2 1 3349 3022 51 6618 1.2 1 3404 3214 52 6701 1.2 1 3473 3228 53 6257 1.2 1 3291 2966 54 6497 1.2 1 3401 3096 55 6598 1.2 1 3510 3088 56 6370 1.2 1 3368 3002 57 5154 1.2 1 2690 2464 58 3266 1.2 1 1681 1585 59 1944 1.2 1 944 1000 60 1138 1.2 1 548 590 61 703 1.2 1 358 345 62 632 1.2 1 306 326 63 525 1.2 1 266 259 64 415 1.2 1 182 233 65 406 1.2 1 179 227 66 475 1.2 1 219 256 67 665 1.2 1 317 348 68 794 1.2 1 405 389 69 840 1.2 1 413 427 70 852 1.2 1 427 425 71 786 1.2 1 368 418 72 769 1.2 1 370 399 73 751 1.2 1 365 386 74 707 1.2 1 306 401 75 609 1.2 1 278 331 76 632 1.2 1 300 332 77 578 1.2 1 288 290 78 464 1.2 1 206 258 79 474 1.2 1 201 273 80 498 1.2 1 177 321 81 477 1.2 1 166 311 82 408 1.2 1 157 251 83 360 1.2 1 116 244 84 379 1.2 1 146 233 85 370 1.2 1 157 213 86 299 1.2 1 93 206 87 284 1.2 1 96 188 88 311 1.2 1 106 205 89 309 1.2 1 135 174 90 268 1.2 1 144 124 91 254 1.2 1 156 98 92 222 1.2 1 127 95 93 213 1.2 1 127 86 94 191 1.2 1 101 90 95 170 1.2 1 100 70 96 158 1.2 1 65 93 97 158 1.2 1 80 78 98 157 1.2 1 81 76 99 160 1.2 1 66 94 100 128 1.2 1 63 65 101 124 1.2 1 63 61 102 163 1.2 1 55 108 103 103 1.2 1 43 60 104 119 1.2 1 53 66 105 90 1.2 1 35 55 106 73 1.2 1 22 51 107 70 1.2 1 22 48 108 75 1.2 1 8 67 109 86 1.2 1 15 71 110 52 1.2 1 10 42 111 79 1.2 1 11 68 112 76 1.2 1 7 69 113 55 1.2 1 5 50 114 60 1.2 1 9 51 115 56 1.2 1 10 46 116 69 1.2 1 17 52 117 50 1.2 1 6 44 118 78 1.2 1 12 66 119 59 1.2 1 4 55 120 72 1.2 1 11 61 121 76 1.2 1 6 70 122 41 1.2 1 9 32 123 61 1.2 1 9 52 124 41 1.2 1 9 32 125 53 1.2 1 6 47 126 66 1.2 1 11 55 127 58 1.2 1 10 48 128 63 1.2 1 10 53 129 76 1.2 1 14 62 130 59 1.2 1 15 44 131 77 1.2 1 21 56 132 71 1.2 1 23 48 133 114 1.2 1 26 88 134 95 1.2 1 32 63 135 81 1.2 1 26 55 136 99 1.2 1 40 59 137 111 1.2 1 38 73 138 115 1.2 1 43 72 139 119 1.2 1 42 77 140 150 1.2 1 48 102 141 233 1.2 1 94 139 142 148 1.2 1 54 94 143 137 1.2 1 55 82 144 206 1.2 1 80 126 145 245 1.2 1 83 162 146 255 1.2 1 90 165 147 510 1.2 1 146 364 148 329 1.2 1 44 285 149 4763 1.2 1 4 4759 150 411825 1.2 1 14 411811 RUN STATISTICS FOR INPUT FILE: DE-3C_trimmed_1.fastq.gz ============================================= 80872082 sequences processed in total