SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684012_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Python version: could not detect Number of cores used for trimming: 2 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 128151). Second best hit was Nextera (count: 0) 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 Output file will be GZIP compressed This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR10684012_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 2743.093 s (16.886 µs/read; 3.55 M reads/minute). === Summary === Total reads processed: 162,448,263 Reads with adapters: 95,488,119 (58.8%) Reads written (passing filters): 162,448,263 (100.0%) Total basepairs processed: 24,529,687,713 bp Quality-trimmed: 94,021,921 bp (0.4%) Total written (filtered): 23,354,977,356 bp (95.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 95488119 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.1% C: 17.3% G: 0.6% T: 31.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 69208960 40612065.8 0 69208960 2 561885 10153016.4 0 561885 3 530955 2538254.1 0 530955 4 445160 634563.5 0 445160 5 465411 158640.9 0 465411 6 409448 39660.2 0 409448 7 399617 9915.1 0 399617 8 515626 2478.8 0 515626 9 294629 619.7 0 293460 1169 10 443489 154.9 1 405581 37908 11 373218 38.7 1 334346 38872 12 434957 9.7 1 375362 59595 13 412477 2.4 1 357175 55302 14 491408 2.4 1 425258 66150 15 333791 2.4 1 288025 45766 16 400595 2.4 1 346519 54076 17 531618 2.4 1 465192 66426 18 247514 2.4 1 213804 33710 19 545952 2.4 1 475903 70049 20 391303 2.4 1 343409 47894 21 236758 2.4 1 205246 31512 22 378512 2.4 1 330138 48374 23 384095 2.4 1 335103 48992 24 517883 2.4 1 453331 64552 25 446795 2.4 1 394010 52785 26 318391 2.4 1 278738 39653 27 244036 2.4 1 211582 32454 28 436036 2.4 1 388761 47275 29 275195 2.4 1 240560 34635 30 449135 2.4 1 400496 48639 31 257323 2.4 1 226108 31215 32 435239 2.4 1 387599 47640 33 363007 2.4 1 322731 40276 34 322304 2.4 1 287800 34504 35 244051 2.4 1 215223 28828 36 341345 2.4 1 303792 37553 37 413893 2.4 1 371845 42048 38 361876 2.4 1 325395 36481 39 191250 2.4 1 167992 23258 40 313347 2.4 1 281078 32269 41 316690 2.4 1 283554 33136 42 359700 2.4 1 322030 37670 43 259080 2.4 1 231757 27323 44 298146 2.4 1 268721 29425 45 324621 2.4 1 291152 33469 46 307464 2.4 1 276570 30894 47 287342 2.4 1 260778 26564 48 254031 2.4 1 228893 25138 49 294190 2.4 1 264410 29780 50 258435 2.4 1 235765 22670 51 253144 2.4 1 230110 23034 52 260887 2.4 1 237246 23641 53 259303 2.4 1 235648 23655 54 314517 2.4 1 287653 26864 55 188436 2.4 1 170931 17505 56 254162 2.4 1 230884 23278 57 345570 2.4 1 315608 29962 58 178314 2.4 1 161678 16636 59 188623 2.4 1 172082 16541 60 271850 2.4 1 248923 22927 61 232654 2.4 1 212939 19715 62 170797 2.4 1 155326 15471 63 427931 2.4 1 395962 31969 64 169401 2.4 1 154584 14817 65 138415 2.4 1 126801 11614 66 133297 2.4 1 122237 11060 67 221693 2.4 1 205777 15916 68 193700 2.4 1 178031 15669 69 176165 2.4 1 162861 13304 70 201419 2.4 1 186827 14592 71 189718 2.4 1 175653 14065 72 187812 2.4 1 173552 14260 73 249710 2.4 1 232376 17334 74 154985 2.4 1 144016 10969 75 151266 2.4 1 141239 10027 76 108750 2.4 1 101057 7693 77 106520 2.4 1 98724 7796 78 113574 2.4 1 105725 7849 79 112816 2.4 1 104923 7893 80 112927 2.4 1 105368 7559 81 110809 2.4 1 103195 7614 82 108897 2.4 1 101512 7385 83 112284 2.4 1 104741 7543 84 106224 2.4 1 99106 7118 85 106624 2.4 1 99724 6900 86 97996 2.4 1 91713 6283 87 91124 2.4 1 85361 5763 88 87735 2.4 1 82147 5588 89 85030 2.4 1 79745 5285 90 83706 2.4 1 78772 4934 91 77560 2.4 1 72861 4699 92 75529 2.4 1 70992 4537 93 72979 2.4 1 68838 4141 94 66568 2.4 1 62797 3771 95 64062 2.4 1 60313 3749 96 61367 2.4 1 57874 3493 97 58014 2.4 1 54714 3300 98 57226 2.4 1 54107 3119 99 55287 2.4 1 52334 2953 100 52705 2.4 1 49971 2734 101 46305 2.4 1 43864 2441 102 41729 2.4 1 39542 2187 103 38356 2.4 1 36376 1980 104 35502 2.4 1 33717 1785 105 33570 2.4 1 31850 1720 106 30692 2.4 1 29191 1501 107 28867 2.4 1 27406 1461 108 25732 2.4 1 24468 1264 109 22889 2.4 1 21840 1049 110 20120 2.4 1 19219 901 111 17860 2.4 1 17034 826 112 15746 2.4 1 15070 676 113 14001 2.4 1 13372 629 114 11745 2.4 1 11234 511 115 10362 2.4 1 9915 447 116 8720 2.4 1 8354 366 117 7269 2.4 1 6971 298 118 5845 2.4 1 5605 240 119 5111 2.4 1 4889 222 120 26228 2.4 1 25022 1206 121 4864 2.4 1 4682 182 122 2253 2.4 1 2165 88 123 1572 2.4 1 1494 78 124 975 2.4 1 934 41 125 623 2.4 1 599 24 126 499 2.4 1 483 16 127 347 2.4 1 315 32 128 244 2.4 1 228 16 129 186 2.4 1 165 21 130 160 2.4 1 144 16 131 118 2.4 1 106 12 132 81 2.4 1 74 7 133 99 2.4 1 90 9 134 69 2.4 1 56 13 135 121 2.4 1 113 8 136 48 2.4 1 43 5 137 68 2.4 1 62 6 138 49 2.4 1 39 10 139 82 2.4 1 71 11 140 54 2.4 1 43 11 141 64 2.4 1 56 8 142 33 2.4 1 23 10 143 35 2.4 1 30 5 144 31 2.4 1 23 8 145 64 2.4 1 45 19 146 27 2.4 1 16 11 147 32 2.4 1 25 7 148 37 2.4 1 27 10 149 40 2.4 1 29 11 150 20 2.4 1 7 13 151 310 2.4 1 211 99 RUN STATISTICS FOR INPUT FILE: ERR10684012_2.fastq.gz ============================================= 162448263 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 162448263 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 143532 (0.09%)