SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065373_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: 452). Second best hit was Nextera (count: 2) 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 SRR10065373_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1862.271 s (21.943 µs/read; 2.73 M reads/minute). === Summary === Total reads processed: 84,868,974 Reads with adapters: 39,978,360 (47.1%) Reads written (passing filters): 84,868,974 (100.0%) Total basepairs processed: 12,730,346,100 bp Quality-trimmed: 105,429,695 bp (0.8%) Total written (filtered): 12,582,676,336 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39978360 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.4% C: 16.7% G: 0.3% T: 32.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 39798893 21217243.5 0 39798893 2 43016 5304310.9 0 43016 3 34642 1326077.7 0 34642 4 13090 331519.4 0 13090 5 6495 82879.9 0 6495 6 4350 20720.0 0 4350 7 4486 5180.0 0 4486 8 3584 1295.0 0 3584 9 3300 323.7 0 3291 9 10 3926 80.9 1 3528 398 11 2953 20.2 1 2541 412 12 3341 5.1 1 3045 296 13 2657 1.3 1 2411 246 14 3486 1.3 1 3141 345 15 1986 1.3 1 1813 173 16 2220 1.3 1 1997 223 17 2793 1.3 1 2563 230 18 1384 1.3 1 1261 123 19 2364 1.3 1 2183 181 20 1467 1.3 1 1343 124 21 1311 1.3 1 1170 141 22 1617 1.3 1 1481 136 23 1591 1.3 1 1438 153 24 2449 1.3 1 2184 265 25 1213 1.3 1 1082 131 26 1101 1.3 1 960 141 27 1052 1.3 1 921 131 28 1416 1.3 1 1240 176 29 923 1.3 1 791 132 30 1451 1.3 1 1280 171 31 587 1.3 1 500 87 32 1046 1.3 1 906 140 33 850 1.3 1 745 105 34 910 1.3 1 769 141 35 679 1.3 1 586 93 36 872 1.3 1 725 147 37 659 1.3 1 546 113 38 574 1.3 1 481 93 39 672 1.3 1 545 127 40 984 1.3 1 801 183 41 436 1.3 1 354 82 42 860 1.3 1 731 129 43 248 1.3 1 196 52 44 674 1.3 1 555 119 45 485 1.3 1 377 108 46 409 1.3 1 321 88 47 553 1.3 1 447 106 48 411 1.3 1 299 112 49 334 1.3 1 244 90 50 394 1.3 1 302 92 51 368 1.3 1 282 86 52 344 1.3 1 256 88 53 368 1.3 1 285 83 54 473 1.3 1 346 127 55 220 1.3 1 175 45 56 308 1.3 1 240 68 57 662 1.3 1 519 143 58 227 1.3 1 173 54 59 188 1.3 1 140 48 60 297 1.3 1 231 66 61 221 1.3 1 150 71 62 224 1.3 1 161 63 63 854 1.3 1 616 238 64 175 1.3 1 120 55 65 143 1.3 1 92 51 66 117 1.3 1 74 43 67 201 1.3 1 152 49 68 244 1.3 1 159 85 69 179 1.3 1 116 63 70 198 1.3 1 125 73 71 205 1.3 1 137 68 72 179 1.3 1 122 57 73 242 1.3 1 157 85 74 294 1.3 1 204 90 75 416 1.3 1 295 121 76 1019 1.3 1 860 159 77 368 1.3 1 281 87 78 172 1.3 1 115 57 79 141 1.3 1 75 66 80 126 1.3 1 70 56 81 85 1.3 1 48 37 82 76 1.3 1 42 34 83 90 1.3 1 44 46 84 93 1.3 1 63 30 85 79 1.3 1 44 35 86 57 1.3 1 32 25 87 67 1.3 1 31 36 88 71 1.3 1 36 35 89 55 1.3 1 38 17 90 45 1.3 1 26 19 91 51 1.3 1 21 30 92 51 1.3 1 25 26 93 56 1.3 1 31 25 94 50 1.3 1 17 33 95 70 1.3 1 38 32 96 38 1.3 1 22 16 97 56 1.3 1 20 36 98 41 1.3 1 18 23 99 34 1.3 1 19 15 100 38 1.3 1 19 19 101 28 1.3 1 14 14 102 38 1.3 1 24 14 103 42 1.3 1 21 21 104 35 1.3 1 17 18 105 29 1.3 1 18 11 106 36 1.3 1 22 14 107 32 1.3 1 13 19 108 20 1.3 1 4 16 109 19 1.3 1 10 9 110 31 1.3 1 14 17 111 30 1.3 1 16 14 112 33 1.3 1 20 13 113 29 1.3 1 20 9 114 27 1.3 1 13 14 115 23 1.3 1 8 15 116 34 1.3 1 17 17 117 23 1.3 1 15 8 118 21 1.3 1 9 12 119 19 1.3 1 10 9 120 25 1.3 1 15 10 121 12 1.3 1 9 3 122 18 1.3 1 12 6 123 19 1.3 1 13 6 124 27 1.3 1 14 13 125 19 1.3 1 11 8 126 14 1.3 1 9 5 127 11 1.3 1 7 4 128 11 1.3 1 4 7 129 3 1.3 1 1 2 130 11 1.3 1 5 6 131 11 1.3 1 4 7 132 5 1.3 1 3 2 133 4 1.3 1 1 3 134 4 1.3 1 1 3 135 6 1.3 1 3 3 137 4 1.3 1 2 2 138 3 1.3 1 2 1 141 2 1.3 1 0 2 143 1 1.3 1 1 144 1 1.3 1 1 147 2 1.3 1 0 2 148 2 1.3 1 0 2 149 6 1.3 1 0 6 150 20 1.3 1 3 17 RUN STATISTICS FOR INPUT FILE: SRR10065373_2.fastq.gz ============================================= 84868974 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 84868974 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 49316 (0.06%)