SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308517_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: 134598). Second best hit was smallRNA (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 ERR12308517_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1433.040 s (17.410 µs/read; 3.45 M reads/minute). === Summary === Total reads processed: 82,309,934 Reads with adapters: 47,001,918 (57.1%) Reads written (passing filters): 82,309,934 (100.0%) Total basepairs processed: 12,428,800,034 bp Quality-trimmed: 64,513,353 bp (0.5%) Total written (filtered): 11,851,405,711 bp (95.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 47001918 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.7% C: 19.5% G: 1.7% T: 29.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 31449836 20577483.5 0 31449836 2 692993 5144370.9 0 692993 3 462872 1286092.7 0 462872 4 339835 321523.2 0 339835 5 359844 80380.8 0 359844 6 319986 20095.2 0 319986 7 309486 5023.8 0 309486 8 369914 1255.9 0 369914 9 211305 314.0 0 210768 537 10 324435 78.5 1 288502 35933 11 283551 19.6 1 254384 29167 12 309115 4.9 1 266559 42556 13 305438 1.2 1 261047 44391 14 356841 1.2 1 302115 54726 15 243179 1.2 1 211776 31403 16 284605 1.2 1 246142 38463 17 374180 1.2 1 327007 47173 18 184520 1.2 1 159372 25148 19 366533 1.2 1 314876 51657 20 278306 1.2 1 242855 35451 21 158553 1.2 1 138026 20527 22 258563 1.2 1 224123 34440 23 254103 1.2 1 219640 34463 24 339959 1.2 1 290409 49550 25 301789 1.2 1 264184 37605 26 182749 1.2 1 157749 25000 27 177733 1.2 1 154468 23265 28 256401 1.2 1 225681 30720 29 211149 1.2 1 186420 24729 30 225662 1.2 1 197628 28034 31 220801 1.2 1 192695 28106 32 221498 1.2 1 192936 28562 33 206917 1.2 1 181404 25513 34 223307 1.2 1 197189 26118 35 209218 1.2 1 186021 23197 36 197488 1.2 1 172970 24518 37 182975 1.2 1 162860 20115 38 198883 1.2 1 176614 22269 39 205122 1.2 1 182839 22283 40 167375 1.2 1 148917 18458 41 176077 1.2 1 156783 19294 42 196376 1.2 1 175800 20576 43 142768 1.2 1 127519 15249 44 172958 1.2 1 153059 19899 45 178614 1.2 1 159021 19593 46 149817 1.2 1 133164 16653 47 160344 1.2 1 143889 16455 48 150884 1.2 1 135254 15630 49 142942 1.2 1 127800 15142 50 142400 1.2 1 128574 13826 51 132628 1.2 1 119691 12937 52 135042 1.2 1 121533 13509 53 130529 1.2 1 118112 12417 54 158258 1.2 1 143733 14525 55 90430 1.2 1 81883 8547 56 122987 1.2 1 111078 11909 57 136344 1.2 1 122581 13763 58 101325 1.2 1 91950 9375 59 103983 1.2 1 95134 8849 60 115278 1.2 1 105031 10247 61 107684 1.2 1 98247 9437 62 89281 1.2 1 81387 7894 63 172266 1.2 1 158159 14107 64 77405 1.2 1 70473 6932 65 61393 1.2 1 56179 5214 66 59532 1.2 1 54508 5024 67 95095 1.2 1 87866 7229 68 83578 1.2 1 76934 6644 69 70143 1.2 1 64626 5517 70 75896 1.2 1 70215 5681 71 70040 1.2 1 64736 5304 72 69771 1.2 1 64551 5220 73 90082 1.2 1 83810 6272 74 64907 1.2 1 59999 4908 75 64624 1.2 1 60133 4491 76 38187 1.2 1 35406 2781 77 35097 1.2 1 32480 2617 78 37841 1.2 1 35169 2672 79 37246 1.2 1 34640 2606 80 36430 1.2 1 33959 2471 81 34893 1.2 1 32439 2454 82 33267 1.2 1 31041 2226 83 32805 1.2 1 30646 2159 84 30831 1.2 1 28751 2080 85 29843 1.2 1 27892 1951 86 27036 1.2 1 25292 1744 87 25071 1.2 1 23420 1651 88 23007 1.2 1 21628 1379 89 22227 1.2 1 20864 1363 90 21179 1.2 1 19967 1212 91 19037 1.2 1 17914 1123 92 17978 1.2 1 16918 1060 93 16880 1.2 1 15865 1015 94 14969 1.2 1 14067 902 95 14277 1.2 1 13454 823 96 13093 1.2 1 12332 761 97 11980 1.2 1 11279 701 98 11537 1.2 1 10908 629 99 11150 1.2 1 10513 637 100 10142 1.2 1 9554 588 101 8599 1.2 1 8093 506 102 7654 1.2 1 7256 398 103 6862 1.2 1 6482 380 104 6113 1.2 1 5766 347 105 5716 1.2 1 5394 322 106 5127 1.2 1 4839 288 107 4624 1.2 1 4380 244 108 4197 1.2 1 3978 219 109 3445 1.2 1 3254 191 110 3213 1.2 1 3027 186 111 2826 1.2 1 2673 153 112 2549 1.2 1 2423 126 113 2315 1.2 1 2193 122 114 2045 1.2 1 1912 133 115 1603 1.2 1 1491 112 116 1416 1.2 1 1331 85 117 1176 1.2 1 1089 87 118 1028 1.2 1 965 63 119 938 1.2 1 869 69 120 1065 1.2 1 992 73 121 745 1.2 1 696 49 122 526 1.2 1 472 54 123 398 1.2 1 347 51 124 349 1.2 1 314 35 125 296 1.2 1 253 43 126 241 1.2 1 197 44 127 206 1.2 1 175 31 128 153 1.2 1 133 20 129 156 1.2 1 128 28 130 136 1.2 1 124 12 131 104 1.2 1 94 10 132 85 1.2 1 71 14 133 84 1.2 1 68 16 134 84 1.2 1 68 16 135 95 1.2 1 71 24 136 63 1.2 1 54 9 137 77 1.2 1 72 5 138 47 1.2 1 35 12 139 55 1.2 1 46 9 140 48 1.2 1 41 7 141 62 1.2 1 54 8 142 42 1.2 1 28 14 143 50 1.2 1 37 13 144 54 1.2 1 32 22 145 56 1.2 1 40 16 146 41 1.2 1 25 16 147 49 1.2 1 35 14 148 45 1.2 1 20 25 149 55 1.2 1 36 19 150 28 1.2 1 15 13 151 274 1.2 1 55 219 RUN STATISTICS FOR INPUT FILE: ERR12308517_2.fastq.gz ============================================= 82309934 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82309934 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 62874 (0.08%)