SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065375_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: 576). 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 SRR10065375_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1576.002 s (19.348 µs/read; 3.10 M reads/minute). === Summary === Total reads processed: 81,453,846 Reads with adapters: 39,498,958 (48.5%) Reads written (passing filters): 81,453,846 (100.0%) Total basepairs processed: 12,218,076,900 bp Quality-trimmed: 92,350,891 bp (0.8%) Total written (filtered): 12,083,419,274 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39498958 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.1% C: 16.7% G: 0.3% T: 31.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 39309212 20363461.5 0 39309212 2 38524 5090865.4 0 38524 3 32647 1272716.3 0 32647 4 14011 318179.1 0 14011 5 6488 79544.8 0 6488 6 4561 19886.2 0 4561 7 4388 4971.5 0 4388 8 3936 1242.9 0 3936 9 3607 310.7 0 3593 14 10 4172 77.7 1 3780 392 11 3490 19.4 1 2996 494 12 3875 4.9 1 3505 370 13 2941 1.2 1 2662 279 14 3821 1.2 1 3472 349 15 2419 1.2 1 2231 188 16 2500 1.2 1 2253 247 17 3027 1.2 1 2786 241 18 1658 1.2 1 1513 145 19 2793 1.2 1 2589 204 20 1825 1.2 1 1661 164 21 1672 1.2 1 1491 181 22 1929 1.2 1 1769 160 23 1862 1.2 1 1685 177 24 2910 1.2 1 2607 303 25 1479 1.2 1 1315 164 26 1387 1.2 1 1219 168 27 1374 1.2 1 1191 183 28 1769 1.2 1 1561 208 29 1179 1.2 1 1019 160 30 2006 1.2 1 1775 231 31 779 1.2 1 658 121 32 1398 1.2 1 1240 158 33 960 1.2 1 846 114 34 1281 1.2 1 1119 162 35 1151 1.2 1 993 158 36 914 1.2 1 790 124 37 1075 1.2 1 905 170 38 777 1.2 1 659 118 39 996 1.2 1 861 135 40 726 1.2 1 635 91 41 764 1.2 1 625 139 42 894 1.2 1 777 117 43 601 1.2 1 522 79 44 748 1.2 1 639 109 45 682 1.2 1 568 114 46 573 1.2 1 454 119 47 791 1.2 1 691 100 48 605 1.2 1 479 126 49 545 1.2 1 446 99 50 551 1.2 1 446 105 51 480 1.2 1 399 81 52 456 1.2 1 374 82 53 562 1.2 1 467 95 54 670 1.2 1 540 130 55 295 1.2 1 230 65 56 428 1.2 1 361 67 57 811 1.2 1 651 160 58 334 1.2 1 260 74 59 264 1.2 1 200 64 60 412 1.2 1 337 75 61 279 1.2 1 226 53 62 267 1.2 1 201 66 63 995 1.2 1 760 235 64 225 1.2 1 156 69 65 231 1.2 1 175 56 66 167 1.2 1 122 45 67 280 1.2 1 222 58 68 283 1.2 1 201 82 69 245 1.2 1 182 63 70 260 1.2 1 198 62 71 267 1.2 1 190 77 72 289 1.2 1 223 66 73 317 1.2 1 239 78 74 363 1.2 1 271 92 75 531 1.2 1 402 129 76 1366 1.2 1 1173 193 77 469 1.2 1 380 89 78 237 1.2 1 158 79 79 133 1.2 1 83 50 80 124 1.2 1 85 39 81 108 1.2 1 53 55 82 101 1.2 1 54 47 83 104 1.2 1 62 42 84 87 1.2 1 48 39 85 101 1.2 1 58 43 86 102 1.2 1 53 49 87 101 1.2 1 61 40 88 90 1.2 1 46 44 89 63 1.2 1 37 26 90 80 1.2 1 43 37 91 73 1.2 1 32 41 92 62 1.2 1 34 28 93 71 1.2 1 40 31 94 70 1.2 1 36 34 95 83 1.2 1 40 43 96 57 1.2 1 26 31 97 52 1.2 1 26 26 98 46 1.2 1 23 23 99 64 1.2 1 32 32 100 51 1.2 1 28 23 101 44 1.2 1 26 18 102 52 1.2 1 26 26 103 51 1.2 1 29 22 104 52 1.2 1 30 22 105 35 1.2 1 19 16 106 39 1.2 1 22 17 107 33 1.2 1 20 13 108 32 1.2 1 20 12 109 36 1.2 1 18 18 110 34 1.2 1 12 22 111 45 1.2 1 27 18 112 39 1.2 1 21 18 113 37 1.2 1 19 18 114 40 1.2 1 19 21 115 43 1.2 1 26 17 116 31 1.2 1 16 15 117 39 1.2 1 22 17 118 38 1.2 1 14 24 119 30 1.2 1 20 10 120 39 1.2 1 17 22 121 22 1.2 1 9 13 122 24 1.2 1 16 8 123 22 1.2 1 9 13 124 33 1.2 1 20 13 125 24 1.2 1 13 11 126 15 1.2 1 11 4 127 14 1.2 1 5 9 128 13 1.2 1 10 3 129 17 1.2 1 11 6 130 15 1.2 1 4 11 131 9 1.2 1 5 4 132 11 1.2 1 7 4 133 7 1.2 1 1 6 134 7 1.2 1 4 3 135 5 1.2 1 3 2 136 5 1.2 1 3 2 137 3 1.2 1 1 2 138 1 1.2 1 1 139 1 1.2 1 1 140 3 1.2 1 1 2 141 1 1.2 1 0 1 142 1 1.2 1 1 143 2 1.2 1 2 146 3 1.2 1 1 2 147 2 1.2 1 0 2 148 2 1.2 1 1 1 149 4 1.2 1 0 4 150 24 1.2 1 4 20 RUN STATISTICS FOR INPUT FILE: SRR10065375_2.fastq.gz ============================================= 81453846 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 81453846 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 41431 (0.05%)