SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245606_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: 5716). 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 SRR18245606_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3750.939 s (53.934 µs/read; 1.11 M reads/minute). === Summary === Total reads processed: 69,547,451 Reads with adapters: 36,315,595 (52.2%) Reads written (passing filters): 69,547,451 (100.0%) Total basepairs processed: 10,432,117,650 bp Quality-trimmed: 32,152,403 bp (0.3%) Total written (filtered): 10,328,042,617 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36315595 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.5% C: 16.6% G: 0.4% T: 30.2% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 35726192 17386862.8 0 35726192 2 39526 4346715.7 0 39526 3 46270 1086678.9 0 46270 4 18784 271669.7 0 18784 5 9768 67917.4 0 9768 6 7855 16979.4 0 7855 7 8237 4244.8 0 8237 8 8526 1061.2 0 8526 9 6913 265.3 0 6910 3 10 7667 66.3 1 7255 412 11 7342 16.6 1 6739 603 12 7618 4.1 1 7113 505 13 6689 1.0 1 6289 400 14 7404 1.0 1 6886 518 15 6386 1.0 1 6028 358 16 5968 1.0 1 5622 346 17 7767 1.0 1 7285 482 18 4482 1.0 1 4231 251 19 7571 1.0 1 7121 450 20 4908 1.0 1 4618 290 21 4644 1.0 1 4359 285 22 5263 1.0 1 4968 295 23 5127 1.0 1 4820 307 24 6102 1.0 1 5689 413 25 5394 1.0 1 5119 275 26 4257 1.0 1 4003 254 27 4164 1.0 1 3816 348 28 4828 1.0 1 4586 242 29 4103 1.0 1 3843 260 30 4378 1.0 1 4150 228 31 3957 1.0 1 3739 218 32 3880 1.0 1 3697 183 33 3911 1.0 1 3657 254 34 4044 1.0 1 3792 252 35 3544 1.0 1 3367 177 36 5444 1.0 1 5134 310 37 3388 1.0 1 3217 171 38 2590 1.0 1 2376 214 39 4854 1.0 1 4680 174 40 4417 1.0 1 4210 207 41 1634 1.0 1 1487 147 42 4857 1.0 1 4670 187 43 1468 1.0 1 1355 113 44 5013 1.0 1 4833 180 45 2937 1.0 1 2815 122 46 1596 1.0 1 1507 89 47 3830 1.0 1 3693 137 48 2163 1.0 1 2081 82 49 1716 1.0 1 1631 85 50 2080 1.0 1 2015 65 51 1490 1.0 1 1407 83 52 1398 1.0 1 1352 46 53 1981 1.0 1 1925 56 54 2663 1.0 1 2589 74 55 1482 1.0 1 1412 70 56 2000 1.0 1 1939 61 57 3799 1.0 1 3702 97 58 1757 1.0 1 1683 74 59 1591 1.0 1 1536 55 60 2660 1.0 1 2577 83 61 1678 1.0 1 1625 53 62 1464 1.0 1 1422 42 63 2602 1.0 1 2533 69 64 2692 1.0 1 2610 82 65 2083 1.0 1 2038 45 66 2078 1.0 1 2018 60 67 2859 1.0 1 2779 80 68 1805 1.0 1 1754 51 69 1894 1.0 1 1844 50 70 2175 1.0 1 2125 50 71 1425 1.0 1 1384 41 72 849 1.0 1 820 29 73 685 1.0 1 655 30 74 529 1.0 1 512 17 75 508 1.0 1 485 23 76 692 1.0 1 661 31 77 735 1.0 1 710 25 78 845 1.0 1 818 27 79 1074 1.0 1 1043 31 80 1159 1.0 1 1121 38 81 1193 1.0 1 1160 33 82 1270 1.0 1 1238 32 83 1406 1.0 1 1374 32 84 1313 1.0 1 1276 37 85 1518 1.0 1 1472 46 86 1347 1.0 1 1321 26 87 1267 1.0 1 1226 41 88 1271 1.0 1 1233 38 89 1237 1.0 1 1206 31 90 1278 1.0 1 1243 35 91 1193 1.0 1 1153 40 92 1246 1.0 1 1213 33 93 1195 1.0 1 1163 32 94 1169 1.0 1 1132 37 95 1204 1.0 1 1166 38 96 1162 1.0 1 1125 37 97 1171 1.0 1 1144 27 98 1279 1.0 1 1241 38 99 1248 1.0 1 1216 32 100 1323 1.0 1 1295 28 101 1170 1.0 1 1143 27 102 1119 1.0 1 1092 27 103 1175 1.0 1 1143 32 104 1115 1.0 1 1079 36 105 1173 1.0 1 1147 26 106 1075 1.0 1 1042 33 107 1130 1.0 1 1097 33 108 1098 1.0 1 1060 38 109 1057 1.0 1 1030 27 110 1105 1.0 1 1071 34 111 1103 1.0 1 1063 40 112 1072 1.0 1 1032 40 113 1091 1.0 1 1050 41 114 1051 1.0 1 1016 35 115 950 1.0 1 918 32 116 927 1.0 1 882 45 117 869 1.0 1 824 45 118 937 1.0 1 877 60 119 893 1.0 1 820 73 120 1005 1.0 1 868 137 121 975 1.0 1 788 187 122 1076 1.0 1 829 247 123 1243 1.0 1 918 325 124 1240 1.0 1 785 455 125 1344 1.0 1 770 574 126 1525 1.0 1 813 712 127 1429 1.0 1 624 805 128 1521 1.0 1 653 868 129 1629 1.0 1 781 848 130 1500 1.0 1 681 819 131 1363 1.0 1 671 692 132 1266 1.0 1 724 542 133 1302 1.0 1 776 526 134 1208 1.0 1 695 513 135 1179 1.0 1 689 490 136 1230 1.0 1 645 585 137 1196 1.0 1 693 503 138 1302 1.0 1 875 427 139 1285 1.0 1 959 326 140 1560 1.0 1 1267 293 141 2133 1.0 1 1936 197 142 2345 1.0 1 2214 131 143 3132 1.0 1 3003 129 144 4575 1.0 1 4436 139 145 8265 1.0 1 8099 166 146 5153 1.0 1 5038 115 147 1389 1.0 1 1330 59 148 22731 1.0 1 22481 250 149 8223 1.0 1 8085 138 150 72763 1.0 1 71894 869 RUN STATISTICS FOR INPUT FILE: SRR18245606_2.fastq.gz ============================================= 69547451 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 69547451 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 159323 (0.23%)