SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065364_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: 437). 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 SRR10065364_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1879.788 s (23.551 µs/read; 2.55 M reads/minute). === Summary === Total reads processed: 79,818,903 Reads with adapters: 37,991,302 (47.6%) Reads written (passing filters): 79,818,903 (100.0%) Total basepairs processed: 11,972,835,450 bp Quality-trimmed: 95,629,944 bp (0.8%) Total written (filtered): 11,837,046,426 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 37991302 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.7% C: 16.6% G: 0.3% T: 32.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37828834 19954725.8 0 37828834 2 40805 4988681.4 0 40805 3 31858 1247170.4 0 31858 4 12208 311792.6 0 12208 5 5376 77948.1 0 5376 6 3423 19487.0 0 3423 7 3536 4871.8 0 3536 8 2903 1217.9 0 2903 9 2703 304.5 0 2697 6 10 3347 76.1 1 3015 332 11 2593 19.0 1 2158 435 12 2721 4.8 1 2466 255 13 2229 1.2 1 1973 256 14 2848 1.2 1 2552 296 15 1629 1.2 1 1459 170 16 1840 1.2 1 1640 200 17 2235 1.2 1 2015 220 18 1201 1.2 1 1080 121 19 1898 1.2 1 1742 156 20 1300 1.2 1 1169 131 21 1075 1.2 1 955 120 22 1346 1.2 1 1213 133 23 1282 1.2 1 1146 136 24 2290 1.2 1 1977 313 25 957 1.2 1 803 154 26 990 1.2 1 844 146 27 851 1.2 1 691 160 28 1188 1.2 1 1028 160 29 756 1.2 1 636 120 30 1399 1.2 1 1204 195 31 470 1.2 1 367 103 32 961 1.2 1 815 146 33 716 1.2 1 597 119 34 679 1.2 1 557 122 35 745 1.2 1 626 119 36 771 1.2 1 643 128 37 562 1.2 1 469 93 38 917 1.2 1 760 157 39 513 1.2 1 399 114 40 455 1.2 1 365 90 41 485 1.2 1 380 105 42 557 1.2 1 439 118 43 347 1.2 1 278 69 44 551 1.2 1 447 104 45 516 1.2 1 384 132 46 390 1.2 1 300 90 47 482 1.2 1 382 100 48 402 1.2 1 280 122 49 427 1.2 1 317 110 50 368 1.2 1 287 81 51 362 1.2 1 271 91 52 352 1.2 1 263 89 53 369 1.2 1 272 97 54 475 1.2 1 347 128 55 231 1.2 1 167 64 56 339 1.2 1 244 95 57 666 1.2 1 475 191 58 229 1.2 1 171 58 59 200 1.2 1 153 47 60 310 1.2 1 233 77 61 235 1.2 1 163 72 62 259 1.2 1 176 83 63 828 1.2 1 604 224 64 195 1.2 1 130 65 65 139 1.2 1 91 48 66 107 1.2 1 74 33 67 221 1.2 1 148 73 68 228 1.2 1 171 57 69 228 1.2 1 139 89 70 224 1.2 1 153 71 71 243 1.2 1 168 75 72 226 1.2 1 141 85 73 271 1.2 1 193 78 74 376 1.2 1 261 115 75 506 1.2 1 339 167 76 1195 1.2 1 1009 186 77 419 1.2 1 327 92 78 174 1.2 1 110 64 79 144 1.2 1 85 59 80 101 1.2 1 56 45 81 102 1.2 1 51 51 82 101 1.2 1 58 43 83 112 1.2 1 51 61 84 80 1.2 1 47 33 85 95 1.2 1 55 40 86 111 1.2 1 65 46 87 74 1.2 1 37 37 88 88 1.2 1 46 42 89 82 1.2 1 46 36 90 62 1.2 1 30 32 91 68 1.2 1 32 36 92 76 1.2 1 39 37 93 67 1.2 1 30 37 94 64 1.2 1 20 44 95 51 1.2 1 29 22 96 56 1.2 1 28 28 97 67 1.2 1 39 28 98 49 1.2 1 22 27 99 47 1.2 1 24 23 100 52 1.2 1 25 27 101 43 1.2 1 19 24 102 44 1.2 1 18 26 103 38 1.2 1 23 15 104 39 1.2 1 21 18 105 33 1.2 1 17 16 106 33 1.2 1 18 15 107 38 1.2 1 24 14 108 40 1.2 1 23 17 109 32 1.2 1 17 15 110 37 1.2 1 20 17 111 39 1.2 1 16 23 112 27 1.2 1 12 15 113 35 1.2 1 18 17 114 43 1.2 1 22 21 115 24 1.2 1 14 10 116 36 1.2 1 18 18 117 48 1.2 1 30 18 118 29 1.2 1 18 11 119 37 1.2 1 21 16 120 31 1.2 1 12 19 121 24 1.2 1 14 10 122 28 1.2 1 17 11 123 30 1.2 1 10 20 124 26 1.2 1 8 18 125 19 1.2 1 10 9 126 14 1.2 1 12 2 127 16 1.2 1 6 10 128 9 1.2 1 6 3 129 16 1.2 1 6 10 130 16 1.2 1 7 9 131 9 1.2 1 5 4 132 5 1.2 1 1 4 133 3 1.2 1 1 2 134 12 1.2 1 8 4 135 5 1.2 1 2 3 136 2 1.2 1 2 138 3 1.2 1 2 1 139 2 1.2 1 2 140 1 1.2 1 1 141 2 1.2 1 1 1 142 1 1.2 1 1 146 2 1.2 1 0 2 147 2 1.2 1 2 148 2 1.2 1 0 2 149 5 1.2 1 0 5 150 31 1.2 1 1 30 RUN STATISTICS FOR INPUT FILE: SRR10065364_2.fastq.gz ============================================= 79818903 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 79818903 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 43560 (0.05%)