SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065371_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: 524). 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 SRR10065371_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1919.217 s (21.073 µs/read; 2.85 M reads/minute). === Summary === Total reads processed: 91,076,777 Reads with adapters: 43,280,887 (47.5%) Reads written (passing filters): 91,076,777 (100.0%) Total basepairs processed: 13,661,516,550 bp Quality-trimmed: 104,717,827 bp (0.8%) Total written (filtered): 13,510,480,531 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43280887 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.5% C: 16.5% G: 0.3% T: 32.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 43071327 22769194.2 0 43071327 2 44151 5692298.6 0 44151 3 36658 1423074.6 0 36658 4 15972 355768.7 0 15972 5 7086 88942.2 0 7086 6 4960 22235.5 0 4960 7 5194 5558.9 0 5194 8 4197 1389.7 0 4197 9 3869 347.4 0 3860 9 10 4576 86.9 1 4153 423 11 3719 21.7 1 3236 483 12 4105 5.4 1 3695 410 13 3101 1.4 1 2841 260 14 4336 1.4 1 3951 385 15 2428 1.4 1 2220 208 16 2754 1.4 1 2499 255 17 3403 1.4 1 3136 267 18 1761 1.4 1 1639 122 19 2945 1.4 1 2728 217 20 1908 1.4 1 1739 169 21 1688 1.4 1 1546 142 22 2122 1.4 1 1936 186 23 1979 1.4 1 1803 176 24 3203 1.4 1 2886 317 25 1474 1.4 1 1320 154 26 1472 1.4 1 1306 166 27 1284 1.4 1 1116 168 28 1798 1.4 1 1615 183 29 1305 1.4 1 1143 162 30 2083 1.4 1 1835 248 31 888 1.4 1 762 126 32 1470 1.4 1 1304 166 33 1017 1.4 1 909 108 34 1786 1.4 1 1556 230 35 935 1.4 1 777 158 36 920 1.4 1 796 124 37 1017 1.4 1 856 161 38 972 1.4 1 843 129 39 858 1.4 1 728 130 40 879 1.4 1 756 123 41 787 1.4 1 667 120 42 922 1.4 1 798 124 43 677 1.4 1 588 89 44 754 1.4 1 628 126 45 713 1.4 1 587 126 46 678 1.4 1 570 108 47 786 1.4 1 704 82 48 630 1.4 1 484 146 49 665 1.4 1 570 95 50 602 1.4 1 486 116 51 549 1.4 1 442 107 52 471 1.4 1 388 83 53 525 1.4 1 423 102 54 713 1.4 1 579 134 55 386 1.4 1 330 56 56 491 1.4 1 405 86 57 825 1.4 1 663 162 58 387 1.4 1 306 81 59 294 1.4 1 246 48 60 419 1.4 1 346 73 61 337 1.4 1 271 66 62 335 1.4 1 263 72 63 1030 1.4 1 811 219 64 245 1.4 1 174 71 65 231 1.4 1 176 55 66 189 1.4 1 143 46 67 299 1.4 1 238 61 68 300 1.4 1 225 75 69 273 1.4 1 202 71 70 293 1.4 1 217 76 71 307 1.4 1 224 83 72 335 1.4 1 238 97 73 361 1.4 1 268 93 74 426 1.4 1 307 119 75 577 1.4 1 432 145 76 1496 1.4 1 1321 175 77 514 1.4 1 422 92 78 208 1.4 1 138 70 79 163 1.4 1 106 57 80 138 1.4 1 76 62 81 134 1.4 1 78 56 82 114 1.4 1 70 44 83 117 1.4 1 64 53 84 92 1.4 1 45 47 85 114 1.4 1 55 59 86 92 1.4 1 51 41 87 89 1.4 1 43 46 88 114 1.4 1 66 48 89 86 1.4 1 48 38 90 88 1.4 1 48 40 91 91 1.4 1 45 46 92 83 1.4 1 40 43 93 85 1.4 1 48 37 94 79 1.4 1 39 40 95 72 1.4 1 37 35 96 73 1.4 1 41 32 97 63 1.4 1 25 38 98 44 1.4 1 22 22 99 61 1.4 1 33 28 100 68 1.4 1 38 30 101 49 1.4 1 26 23 102 46 1.4 1 29 17 103 49 1.4 1 30 19 104 60 1.4 1 35 25 105 30 1.4 1 15 15 106 62 1.4 1 35 27 107 50 1.4 1 25 25 108 33 1.4 1 21 12 109 37 1.4 1 21 16 110 34 1.4 1 20 14 111 46 1.4 1 23 23 112 45 1.4 1 27 18 113 28 1.4 1 14 14 114 43 1.4 1 20 23 115 35 1.4 1 17 18 116 39 1.4 1 19 20 117 40 1.4 1 25 15 118 35 1.4 1 21 14 119 40 1.4 1 24 16 120 45 1.4 1 25 20 121 41 1.4 1 26 15 122 32 1.4 1 19 13 123 29 1.4 1 16 13 124 27 1.4 1 16 11 125 27 1.4 1 14 13 126 24 1.4 1 13 11 127 12 1.4 1 6 6 128 19 1.4 1 9 10 129 20 1.4 1 9 11 130 20 1.4 1 9 11 131 11 1.4 1 6 5 132 17 1.4 1 11 6 133 6 1.4 1 3 3 134 10 1.4 1 7 3 135 7 1.4 1 5 2 136 4 1.4 1 3 1 137 6 1.4 1 3 3 138 3 1.4 1 0 3 139 2 1.4 1 2 144 1 1.4 1 0 1 145 2 1.4 1 0 2 146 3 1.4 1 1 2 147 2 1.4 1 0 2 148 2 1.4 1 0 2 149 3 1.4 1 1 2 150 21 1.4 1 2 19 RUN STATISTICS FOR INPUT FILE: SRR10065371_2.fastq.gz ============================================= 91076777 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 91076777 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 44721 (0.05%)