SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245605_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: 6684). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245605_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3530.408 s (54.298 µs/read; 1.11 M reads/minute). === Summary === Total reads processed: 65,019,432 Reads with adapters: 34,016,235 (52.3%) Reads written (passing filters): 65,019,432 (100.0%) Total basepairs processed: 9,752,914,800 bp Quality-trimmed: 31,821,969 bp (0.3%) Total written (filtered): 9,648,843,619 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34016235 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.4% C: 16.7% G: 0.5% T: 30.2% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 33370739 16254858.0 0 33370739 2 43119 4063714.5 0 43119 3 51210 1015928.6 0 51210 4 20688 253982.2 0 20688 5 10904 63495.5 0 10904 6 8700 15873.9 0 8700 7 9021 3968.5 0 9021 8 9176 992.1 0 9176 9 8072 248.0 0 8062 10 10 8367 62.0 1 7895 472 11 7996 15.5 1 7314 682 12 8334 3.9 1 7777 557 13 7289 1.0 1 6809 480 14 8423 1.0 1 7874 549 15 6977 1.0 1 6545 432 16 6473 1.0 1 6123 350 17 8490 1.0 1 7956 534 18 4766 1.0 1 4462 304 19 8462 1.0 1 7948 514 20 5481 1.0 1 5170 311 21 5004 1.0 1 4683 321 22 5789 1.0 1 5465 324 23 5668 1.0 1 5355 313 24 6808 1.0 1 6396 412 25 5930 1.0 1 5670 260 26 4649 1.0 1 4341 308 27 4574 1.0 1 4215 359 28 5230 1.0 1 4980 250 29 4486 1.0 1 4169 317 30 5013 1.0 1 4808 205 31 4117 1.0 1 3865 252 32 4548 1.0 1 4330 218 33 4083 1.0 1 3832 251 34 5589 1.0 1 5153 436 35 7863 1.0 1 7488 375 36 3937 1.0 1 3664 273 37 2004 1.0 1 1899 105 38 2424 1.0 1 2288 136 39 4938 1.0 1 4757 181 40 3593 1.0 1 3381 212 41 1788 1.0 1 1695 93 42 5712 1.0 1 5514 198 43 2021 1.0 1 1899 122 44 6657 1.0 1 6448 209 45 4143 1.0 1 3991 152 46 2022 1.0 1 1928 94 47 4691 1.0 1 4556 135 48 2551 1.0 1 2452 99 49 2030 1.0 1 1930 100 50 2026 1.0 1 1960 66 51 1622 1.0 1 1534 88 52 1227 1.0 1 1179 48 53 2011 1.0 1 1940 71 54 2997 1.0 1 2898 99 55 1706 1.0 1 1612 94 56 2175 1.0 1 2089 86 57 4029 1.0 1 3933 96 58 2064 1.0 1 1981 83 59 1754 1.0 1 1696 58 60 3070 1.0 1 2979 91 61 1998 1.0 1 1937 61 62 1745 1.0 1 1697 48 63 3125 1.0 1 3047 78 64 3950 1.0 1 3850 100 65 3079 1.0 1 2998 81 66 3057 1.0 1 2999 58 67 3824 1.0 1 3758 66 68 2170 1.0 1 2113 57 69 2032 1.0 1 1988 44 70 1998 1.0 1 1961 37 71 1179 1.0 1 1146 33 72 644 1.0 1 613 31 73 506 1.0 1 480 26 74 484 1.0 1 458 26 75 493 1.0 1 474 19 76 822 1.0 1 802 20 77 768 1.0 1 749 19 78 768 1.0 1 737 31 79 1061 1.0 1 1029 32 80 1151 1.0 1 1115 36 81 1355 1.0 1 1320 35 82 1465 1.0 1 1434 31 83 1706 1.0 1 1671 35 84 1653 1.0 1 1612 41 85 1864 1.0 1 1818 46 86 1607 1.0 1 1568 39 87 1476 1.0 1 1422 54 88 1405 1.0 1 1364 41 89 1470 1.0 1 1431 39 90 1492 1.0 1 1452 40 91 1357 1.0 1 1326 31 92 1373 1.0 1 1348 25 93 1372 1.0 1 1343 29 94 1358 1.0 1 1327 31 95 1391 1.0 1 1358 33 96 1293 1.0 1 1261 32 97 1241 1.0 1 1207 34 98 1429 1.0 1 1387 42 99 1474 1.0 1 1445 29 100 1483 1.0 1 1449 34 101 1342 1.0 1 1308 34 102 1313 1.0 1 1289 24 103 1175 1.0 1 1144 31 104 1176 1.0 1 1139 37 105 1165 1.0 1 1138 27 106 1206 1.0 1 1176 30 107 1196 1.0 1 1166 30 108 1135 1.0 1 1111 24 109 1070 1.0 1 1043 27 110 1188 1.0 1 1152 36 111 1156 1.0 1 1131 25 112 1102 1.0 1 1066 36 113 1124 1.0 1 1082 42 114 1022 1.0 1 981 41 115 957 1.0 1 923 34 116 991 1.0 1 956 35 117 1023 1.0 1 971 52 118 948 1.0 1 886 62 119 997 1.0 1 889 108 120 1075 1.0 1 959 116 121 1020 1.0 1 843 177 122 1092 1.0 1 865 227 123 1312 1.0 1 957 355 124 1263 1.0 1 791 472 125 1402 1.0 1 830 572 126 1546 1.0 1 824 722 127 1466 1.0 1 705 761 128 1559 1.0 1 690 869 129 1678 1.0 1 812 866 130 1555 1.0 1 712 843 131 1362 1.0 1 672 690 132 1422 1.0 1 804 618 133 1247 1.0 1 730 517 134 1254 1.0 1 728 526 135 1212 1.0 1 695 517 136 1292 1.0 1 722 570 137 1283 1.0 1 784 499 138 1255 1.0 1 874 381 139 1426 1.0 1 1074 352 140 1597 1.0 1 1362 235 141 2349 1.0 1 2142 207 142 2555 1.0 1 2416 139 143 3399 1.0 1 3272 127 144 4705 1.0 1 4564 141 145 8432 1.0 1 8245 187 146 5289 1.0 1 5189 100 147 1449 1.0 1 1406 43 148 22748 1.0 1 22547 201 149 7987 1.0 1 7865 122 150 78370 1.0 1 77584 786 RUN STATISTICS FOR INPUT FILE: SRR18245605_2.fastq.gz ============================================= 65019432 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 65019432 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 165994 (0.26%)