SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245589_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 5835). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245589_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3754.943 s (47.715 µs/read; 1.26 M reads/minute). === Summary === Total reads processed: 78,694,915 Reads with adapters: 40,930,898 (52.0%) Reads written (passing filters): 78,694,915 (100.0%) Total basepairs processed: 11,804,237,250 bp Quality-trimmed: 35,986,802 bp (0.3%) Total written (filtered): 11,686,404,802 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40930898 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.3% C: 16.6% G: 0.4% T: 30.4% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 40233297 19673728.8 0 40233297 2 47290 4918432.2 0 47290 3 53068 1229608.0 0 53068 4 23129 307402.0 0 23129 5 12322 76850.5 0 12322 6 10511 19212.6 0 10511 7 10555 4803.2 0 10555 8 10842 1200.8 0 10842 9 9469 300.2 0 9462 7 10 10033 75.0 1 9561 472 11 9415 18.8 1 8707 708 12 9467 4.7 1 8936 531 13 8272 1.2 1 7773 499 14 9176 1.2 1 8615 561 15 8104 1.2 1 7650 454 16 7574 1.2 1 7173 401 17 8792 1.2 1 8285 507 18 6251 1.2 1 5956 295 19 8819 1.2 1 8344 475 20 6330 1.2 1 5993 337 21 5811 1.2 1 5479 332 22 6327 1.2 1 6020 307 23 6263 1.2 1 5925 338 24 7309 1.2 1 6856 453 25 6077 1.2 1 5809 268 26 4957 1.2 1 4662 295 27 5041 1.2 1 4665 376 28 5569 1.2 1 5332 237 29 4747 1.2 1 4455 292 30 5249 1.2 1 5004 245 31 4369 1.2 1 4136 233 32 4769 1.2 1 4591 178 33 4270 1.2 1 4082 188 34 4604 1.2 1 4352 252 35 5736 1.2 1 5349 387 36 4275 1.2 1 3935 340 37 3216 1.2 1 3056 160 38 4968 1.2 1 4785 183 39 2619 1.2 1 2420 199 40 3553 1.2 1 3411 142 41 3525 1.2 1 3401 124 42 5104 1.2 1 4847 257 43 2407 1.2 1 2274 133 44 10201 1.2 1 9898 303 45 4256 1.2 1 4065 191 46 1251 1.2 1 1118 133 47 5985 1.2 1 5858 127 48 629 1.2 1 576 53 49 2002 1.2 1 1907 95 50 600 1.2 1 558 42 51 1123 1.2 1 1056 67 52 504 1.2 1 470 34 53 2555 1.2 1 2487 68 54 4223 1.2 1 4097 126 55 914 1.2 1 853 61 56 2540 1.2 1 2450 90 57 8103 1.2 1 7907 196 58 1342 1.2 1 1269 73 59 1108 1.2 1 1060 48 60 5644 1.2 1 5520 124 61 1704 1.2 1 1642 62 62 605 1.2 1 570 35 63 5860 1.2 1 5716 144 64 8002 1.2 1 7817 185 65 1025 1.2 1 983 42 66 1364 1.2 1 1311 53 67 988 1.2 1 962 26 68 382 1.2 1 345 37 69 735 1.2 1 700 35 70 1088 1.2 1 1042 46 71 423 1.2 1 408 15 72 418 1.2 1 385 33 73 526 1.2 1 491 35 74 630 1.2 1 604 26 75 874 1.2 1 841 33 76 1351 1.2 1 1312 39 77 1410 1.2 1 1360 50 78 1481 1.2 1 1428 53 79 1619 1.2 1 1567 52 80 1592 1.2 1 1534 58 81 1552 1.2 1 1500 52 82 1531 1.2 1 1481 50 83 1753 1.2 1 1681 72 84 1632 1.2 1 1592 40 85 1739 1.2 1 1688 51 86 1615 1.2 1 1563 52 87 1547 1.2 1 1487 60 88 1523 1.2 1 1469 54 89 1490 1.2 1 1453 37 90 1428 1.2 1 1396 32 91 1444 1.2 1 1409 35 92 1403 1.2 1 1362 41 93 1399 1.2 1 1359 40 94 1407 1.2 1 1373 34 95 1389 1.2 1 1341 48 96 1370 1.2 1 1338 32 97 1376 1.2 1 1339 37 98 1365 1.2 1 1331 34 99 1443 1.2 1 1410 33 100 1463 1.2 1 1421 42 101 1378 1.2 1 1332 46 102 1294 1.2 1 1262 32 103 1287 1.2 1 1257 30 104 1233 1.2 1 1207 26 105 1250 1.2 1 1217 33 106 1224 1.2 1 1194 30 107 1249 1.2 1 1214 35 108 1200 1.2 1 1166 34 109 1136 1.2 1 1101 35 110 1140 1.2 1 1108 32 111 1223 1.2 1 1175 48 112 1159 1.2 1 1130 29 113 1106 1.2 1 1074 32 114 1069 1.2 1 1020 49 115 1050 1.2 1 1000 50 116 1021 1.2 1 957 64 117 1048 1.2 1 965 83 118 1100 1.2 1 959 141 119 1126 1.2 1 935 191 120 1162 1.2 1 891 271 121 1328 1.2 1 934 394 122 1431 1.2 1 849 582 123 1666 1.2 1 888 778 124 1812 1.2 1 804 1008 125 2062 1.2 1 821 1241 126 2330 1.2 1 803 1527 127 2407 1.2 1 738 1669 128 2493 1.2 1 715 1778 129 2421 1.2 1 699 1722 130 2107 1.2 1 699 1408 131 1731 1.2 1 667 1064 132 1433 1.2 1 711 722 133 1302 1.2 1 671 631 134 1202 1.2 1 695 507 135 1211 1.2 1 646 565 136 1157 1.2 1 619 538 137 1168 1.2 1 703 465 138 1227 1.2 1 846 381 139 1298 1.2 1 1011 287 140 1669 1.2 1 1387 282 141 2304 1.2 1 2097 207 142 2521 1.2 1 2411 110 143 3501 1.2 1 3362 139 144 4997 1.2 1 4858 139 145 9179 1.2 1 9004 175 146 5485 1.2 1 5368 117 147 1461 1.2 1 1423 38 148 25174 1.2 1 24879 295 149 8640 1.2 1 8490 150 150 82319 1.2 1 81480 839 RUN STATISTICS FOR INPUT FILE: SRR18245589_2.fastq.gz ============================================= 78694915 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 78694915 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 181240 (0.23%)