SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065365_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: 653). 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 SRR10065365_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1531.897 s (21.855 µs/read; 2.75 M reads/minute). === Summary === Total reads processed: 70,095,226 Reads with adapters: 33,516,019 (47.8%) Reads written (passing filters): 70,095,226 (100.0%) Total basepairs processed: 10,514,283,900 bp Quality-trimmed: 81,978,397 bp (0.8%) Total written (filtered): 10,396,361,619 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 33516019 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.8% C: 16.7% G: 0.3% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 33343148 17523806.5 0 33343148 2 36813 4380951.6 0 36813 3 30373 1095237.9 0 30373 4 12009 273809.5 0 12009 5 5985 68452.4 0 5985 6 4379 17113.1 0 4379 7 4405 4278.3 0 4405 8 3637 1069.6 0 3637 9 3446 267.4 0 3439 7 10 4191 66.8 1 3769 422 11 3325 16.7 1 2853 472 12 3566 4.2 1 3220 346 13 2896 1.0 1 2618 278 14 3553 1.0 1 3200 353 15 2084 1.0 1 1903 181 16 2316 1.0 1 2099 217 17 2791 1.0 1 2561 230 18 1597 1.0 1 1466 131 19 2495 1.0 1 2305 190 20 1686 1.0 1 1533 153 21 1434 1.0 1 1274 160 22 1814 1.0 1 1665 149 23 1625 1.0 1 1459 166 24 2737 1.0 1 2433 304 25 1167 1.0 1 1015 152 26 1195 1.0 1 1025 170 27 1109 1.0 1 932 177 28 1514 1.0 1 1335 179 29 973 1.0 1 842 131 30 1542 1.0 1 1339 203 31 659 1.0 1 568 91 32 1136 1.0 1 982 154 33 1079 1.0 1 922 157 34 882 1.0 1 749 133 35 919 1.0 1 760 159 36 709 1.0 1 579 130 37 1019 1.0 1 882 137 38 482 1.0 1 410 72 39 729 1.0 1 615 114 40 1036 1.0 1 868 168 41 382 1.0 1 314 68 42 782 1.0 1 670 112 43 413 1.0 1 349 64 44 624 1.0 1 515 109 45 524 1.0 1 434 90 46 415 1.0 1 344 71 47 618 1.0 1 522 96 48 410 1.0 1 291 119 49 411 1.0 1 316 95 50 439 1.0 1 355 84 51 402 1.0 1 319 83 52 350 1.0 1 260 90 53 386 1.0 1 301 85 54 576 1.0 1 431 145 55 233 1.0 1 176 57 56 386 1.0 1 308 78 57 731 1.0 1 568 163 58 252 1.0 1 184 68 59 193 1.0 1 153 40 60 306 1.0 1 224 82 61 248 1.0 1 193 55 62 253 1.0 1 190 63 63 884 1.0 1 640 244 64 258 1.0 1 171 87 65 195 1.0 1 142 53 66 122 1.0 1 83 39 67 227 1.0 1 159 68 68 255 1.0 1 181 74 69 219 1.0 1 156 63 70 179 1.0 1 124 55 71 264 1.0 1 190 74 72 266 1.0 1 193 73 73 282 1.0 1 206 76 74 337 1.0 1 256 81 75 414 1.0 1 291 123 76 1193 1.0 1 1026 167 77 449 1.0 1 343 106 78 191 1.0 1 119 72 79 129 1.0 1 72 57 80 115 1.0 1 64 51 81 113 1.0 1 57 56 82 89 1.0 1 40 49 83 100 1.0 1 54 46 84 74 1.0 1 34 40 85 84 1.0 1 49 35 86 67 1.0 1 47 20 87 72 1.0 1 40 32 88 79 1.0 1 41 38 89 71 1.0 1 38 33 90 64 1.0 1 31 33 91 60 1.0 1 31 29 92 50 1.0 1 21 29 93 48 1.0 1 19 29 94 63 1.0 1 33 30 95 53 1.0 1 26 27 96 55 1.0 1 30 25 97 43 1.0 1 24 19 98 52 1.0 1 27 25 99 52 1.0 1 21 31 100 43 1.0 1 25 18 101 49 1.0 1 28 21 102 35 1.0 1 22 13 103 42 1.0 1 26 16 104 29 1.0 1 16 13 105 35 1.0 1 24 11 106 36 1.0 1 24 12 107 39 1.0 1 25 14 108 31 1.0 1 15 16 109 37 1.0 1 19 18 110 33 1.0 1 16 17 111 24 1.0 1 10 14 112 49 1.0 1 31 18 113 40 1.0 1 17 23 114 21 1.0 1 13 8 115 25 1.0 1 14 11 116 27 1.0 1 15 12 117 31 1.0 1 18 13 118 26 1.0 1 15 11 119 30 1.0 1 18 12 120 18 1.0 1 9 9 121 21 1.0 1 6 15 122 27 1.0 1 12 15 123 25 1.0 1 12 13 124 21 1.0 1 11 10 125 20 1.0 1 10 10 126 22 1.0 1 11 11 127 16 1.0 1 9 7 128 16 1.0 1 5 11 129 14 1.0 1 6 8 130 10 1.0 1 8 2 131 8 1.0 1 3 5 132 9 1.0 1 4 5 133 2 1.0 1 0 2 134 4 1.0 1 2 2 135 4 1.0 1 2 2 136 1 1.0 1 1 137 4 1.0 1 1 3 139 2 1.0 1 0 2 141 2 1.0 1 0 2 143 1 1.0 1 1 146 2 1.0 1 0 2 147 1 1.0 1 0 1 149 3 1.0 1 0 3 150 27 1.0 1 2 25 RUN STATISTICS FOR INPUT FILE: SRR10065365_2.fastq.gz ============================================= 70095226 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 70095226 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36304 (0.05%)