SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245592_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: 36615). 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 SRR18245592_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4426.585 s (54.223 µs/read; 1.11 M reads/minute). === Summary === Total reads processed: 81,636,647 Reads with adapters: 42,301,768 (51.8%) Reads written (passing filters): 81,636,647 (100.0%) Total basepairs processed: 12,245,497,050 bp Quality-trimmed: 29,036,416 bp (0.2%) Total written (filtered): 12,034,415,420 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 42301768 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.3% C: 19.8% G: 0.4% T: 30.3% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 37843815 20409161.8 0 37843815 2 188232 5102290.4 0 188232 3 174772 1275572.6 0 174772 4 155604 318893.2 0 155604 5 143608 79723.3 0 143608 6 122552 19930.8 0 122552 7 125833 4982.7 0 125833 8 134564 1245.7 0 134564 9 88911 311.4 0 88487 424 10 117199 77.9 1 105748 11451 11 110782 19.5 1 98734 12048 12 112499 4.9 1 100667 11832 13 100842 1.2 1 91468 9374 14 105065 1.2 1 93903 11162 15 91223 1.2 1 82138 9085 16 93489 1.2 1 83676 9813 17 104431 1.2 1 94475 9956 18 68673 1.2 1 61796 6877 19 105055 1.2 1 95320 9735 20 73227 1.2 1 66551 6676 21 62702 1.2 1 56269 6433 22 72148 1.2 1 65740 6408 23 69637 1.2 1 63530 6107 24 86685 1.2 1 78583 8102 25 73866 1.2 1 67813 6053 26 48611 1.2 1 44271 4340 27 48893 1.2 1 44483 4410 28 59068 1.2 1 54562 4506 29 52265 1.2 1 47728 4537 30 56362 1.2 1 51991 4371 31 46237 1.2 1 42532 3705 32 49052 1.2 1 45134 3918 33 49076 1.2 1 44941 4135 34 54438 1.2 1 49970 4468 35 42101 1.2 1 38676 3425 36 37738 1.2 1 34171 3567 37 53796 1.2 1 50332 3464 38 34520 1.2 1 31793 2727 39 40922 1.2 1 37866 3056 40 41450 1.2 1 38476 2974 41 19915 1.2 1 17498 2417 42 39555 1.2 1 37126 2429 43 28194 1.2 1 25177 3017 44 86485 1.2 1 82132 4353 45 33829 1.2 1 31275 2554 46 11282 1.2 1 9896 1386 47 34734 1.2 1 33098 1636 48 13590 1.2 1 12456 1134 49 15904 1.2 1 14615 1289 50 12680 1.2 1 11867 813 51 13170 1.2 1 12147 1023 52 9346 1.2 1 8674 672 53 18426 1.2 1 17400 1026 54 25667 1.2 1 24628 1039 55 12803 1.2 1 11899 904 56 18554 1.2 1 17323 1231 57 31835 1.2 1 30549 1286 58 14178 1.2 1 13235 943 59 13411 1.2 1 12615 796 60 23811 1.2 1 22764 1047 61 15929 1.2 1 15193 736 62 9691 1.2 1 9033 658 63 23363 1.2 1 22298 1065 64 29593 1.2 1 28391 1202 65 16902 1.2 1 16155 747 66 17975 1.2 1 17095 880 67 19734 1.2 1 19149 585 68 8502 1.2 1 8039 463 69 11045 1.2 1 10533 512 70 12725 1.2 1 12256 469 71 6703 1.2 1 6374 329 72 4027 1.2 1 3769 258 73 3584 1.2 1 3354 230 74 3689 1.2 1 3436 253 75 4447 1.2 1 4149 298 76 6116 1.2 1 5776 340 77 6455 1.2 1 6041 414 78 7399 1.2 1 7017 382 79 7941 1.2 1 7540 401 80 8174 1.2 1 7812 362 81 8401 1.2 1 7977 424 82 8818 1.2 1 8323 495 83 9909 1.2 1 9452 457 84 9318 1.2 1 8846 472 85 9663 1.2 1 9221 442 86 8834 1.2 1 8415 419 87 7940 1.2 1 7582 358 88 7797 1.2 1 7422 375 89 7631 1.2 1 7260 371 90 7390 1.2 1 7048 342 91 7336 1.2 1 6992 344 92 7077 1.2 1 6779 298 93 7056 1.2 1 6794 262 94 6854 1.2 1 6523 331 95 6813 1.2 1 6489 324 96 6779 1.2 1 6500 279 97 6916 1.2 1 6621 295 98 7174 1.2 1 6894 280 99 7026 1.2 1 6752 274 100 7028 1.2 1 6756 272 101 6668 1.2 1 6411 257 102 6571 1.2 1 6294 277 103 6285 1.2 1 6005 280 104 6233 1.2 1 5988 245 105 6484 1.2 1 6210 274 106 6355 1.2 1 6068 287 107 6283 1.2 1 6018 265 108 6247 1.2 1 5983 264 109 6040 1.2 1 5811 229 110 6342 1.2 1 6088 254 111 6159 1.2 1 5912 247 112 6191 1.2 1 5941 250 113 6257 1.2 1 5987 270 114 6204 1.2 1 5944 260 115 6086 1.2 1 5833 253 116 6152 1.2 1 5907 245 117 6029 1.2 1 5745 284 118 6169 1.2 1 5904 265 119 6031 1.2 1 5727 304 120 6160 1.2 1 5819 341 121 6031 1.2 1 5636 395 122 6234 1.2 1 5694 540 123 6602 1.2 1 5925 677 124 6383 1.2 1 5510 873 125 6596 1.2 1 5439 1157 126 6485 1.2 1 5131 1354 127 6320 1.2 1 4723 1597 128 6267 1.2 1 4506 1761 129 6293 1.2 1 4206 2087 130 6132 1.2 1 3851 2281 131 6474 1.2 1 3721 2753 132 6715 1.2 1 3364 3351 133 6802 1.2 1 3143 3659 134 6505 1.2 1 2796 3709 135 6020 1.2 1 2354 3666 136 5516 1.2 1 2077 3439 137 4399 1.2 1 1919 2480 138 3911 1.2 1 2162 1749 139 3186 1.2 1 1877 1309 140 2798 1.2 1 1825 973 141 2964 1.2 1 2306 658 142 2261 1.2 1 1782 479 143 2475 1.2 1 2004 471 144 2962 1.2 1 2342 620 145 3889 1.2 1 3126 763 146 2090 1.2 1 1563 527 147 436 1.2 1 280 156 148 5180 1.2 1 4382 798 149 1833 1.2 1 1421 412 150 39997 1.2 1 34482 5515 RUN STATISTICS FOR INPUT FILE: SRR18245592_2.fastq.gz ============================================= 81636647 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 81636647 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 139976 (0.17%)