SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308516_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: 104216). 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 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR12308516_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1161.597 s (17.728 µs/read; 3.38 M reads/minute). === Summary === Total reads processed: 65,523,131 Reads with adapters: 36,243,338 (55.3%) Reads written (passing filters): 65,523,131 (100.0%) Total basepairs processed: 9,893,992,781 bp Quality-trimmed: 61,511,738 bp (0.6%) Total written (filtered): 9,533,441,484 bp (96.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36243338 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.5% C: 18.6% G: 0.9% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26764510 16380782.8 0 26764510 2 408194 4095195.7 0 408194 3 294652 1023798.9 0 294652 4 229547 255949.7 0 229547 5 240254 63987.4 0 240254 6 211433 15996.9 0 211433 7 204731 3999.2 0 204731 8 252424 999.8 0 252424 9 133291 250.0 0 132860 431 10 218654 62.5 1 193284 25370 11 190729 15.6 1 170117 20612 12 202150 3.9 1 166112 36038 13 194699 1.0 1 157444 37255 14 231490 1.0 1 183369 48121 15 158259 1.0 1 128712 29547 16 185617 1.0 1 150376 35241 17 240366 1.0 1 197272 43094 18 121141 1.0 1 97996 23145 19 232222 1.0 1 187332 44890 20 183580 1.0 1 149685 33895 21 111099 1.0 1 90991 20108 22 169157 1.0 1 137606 31551 23 167313 1.0 1 135636 31677 24 193390 1.0 1 155932 37458 25 200886 1.0 1 164389 36497 26 127510 1.0 1 103682 23828 27 124511 1.0 1 101614 22897 28 164319 1.0 1 136092 28227 29 132507 1.0 1 109929 22578 30 162512 1.0 1 133536 28976 31 124351 1.0 1 102655 21696 32 141588 1.0 1 116834 24754 33 128970 1.0 1 106913 22057 34 134897 1.0 1 111677 23220 35 173029 1.0 1 143312 29717 36 160433 1.0 1 135053 25380 37 110355 1.0 1 92519 17836 38 94935 1.0 1 79978 14957 39 98353 1.0 1 83048 15305 40 89490 1.0 1 74989 14501 41 113823 1.0 1 95593 18230 42 114869 1.0 1 97199 17670 43 92730 1.0 1 77662 15068 44 100051 1.0 1 84215 15836 45 106401 1.0 1 89241 17160 46 94977 1.0 1 80223 14754 47 92229 1.0 1 78586 13643 48 82134 1.0 1 69882 12252 49 87134 1.0 1 73937 13197 50 79313 1.0 1 68068 11245 51 77775 1.0 1 66416 11359 52 76897 1.0 1 65862 11035 53 73470 1.0 1 63338 10132 54 82931 1.0 1 71438 11493 55 56575 1.0 1 48991 7584 56 67824 1.0 1 58327 9497 57 83605 1.0 1 71901 11704 58 48787 1.0 1 41907 6880 59 51586 1.0 1 44931 6655 60 63220 1.0 1 54996 8224 61 56886 1.0 1 49574 7312 62 42431 1.0 1 36988 5443 63 85461 1.0 1 74925 10536 64 40065 1.0 1 34881 5184 65 31080 1.0 1 27094 3986 66 30187 1.0 1 26397 3790 67 46332 1.0 1 41176 5156 68 40156 1.0 1 35462 4694 69 33878 1.0 1 29969 3909 70 37066 1.0 1 33026 4040 71 33645 1.0 1 29896 3749 72 32211 1.0 1 28689 3522 73 41418 1.0 1 37016 4402 74 29444 1.0 1 26350 3094 75 28564 1.0 1 25777 2787 76 15739 1.0 1 14118 1621 77 15747 1.0 1 14050 1697 78 16656 1.0 1 14972 1684 79 16322 1.0 1 14698 1624 80 15913 1.0 1 14335 1578 81 15088 1.0 1 13540 1548 82 14075 1.0 1 12685 1390 83 13990 1.0 1 12622 1368 84 12874 1.0 1 11620 1254 85 12378 1.0 1 11213 1165 86 11106 1.0 1 10133 973 87 10013 1.0 1 9094 919 88 9085 1.0 1 8284 801 89 8865 1.0 1 8105 760 90 8465 1.0 1 7730 735 91 7763 1.0 1 7093 670 92 6987 1.0 1 6427 560 93 6536 1.0 1 5970 566 94 5928 1.0 1 5462 466 95 5560 1.0 1 5137 423 96 5012 1.0 1 4620 392 97 4709 1.0 1 4339 370 98 4369 1.0 1 4040 329 99 4319 1.0 1 3987 332 100 3869 1.0 1 3580 289 101 3228 1.0 1 2973 255 102 2963 1.0 1 2752 211 103 2522 1.0 1 2346 176 104 2343 1.0 1 2175 168 105 2208 1.0 1 2031 177 106 1877 1.0 1 1747 130 107 1786 1.0 1 1682 104 108 1560 1.0 1 1458 102 109 1406 1.0 1 1289 117 110 1128 1.0 1 1048 80 111 1085 1.0 1 1020 65 112 936 1.0 1 869 67 113 814 1.0 1 755 59 114 696 1.0 1 654 42 115 583 1.0 1 541 42 116 467 1.0 1 436 31 117 385 1.0 1 359 26 118 375 1.0 1 347 28 119 329 1.0 1 299 30 120 348 1.0 1 318 30 121 268 1.0 1 237 31 122 188 1.0 1 163 25 123 161 1.0 1 149 12 124 132 1.0 1 117 15 125 140 1.0 1 126 14 126 113 1.0 1 99 14 127 105 1.0 1 85 20 128 78 1.0 1 64 14 129 76 1.0 1 61 15 130 69 1.0 1 61 8 131 84 1.0 1 72 12 132 48 1.0 1 37 11 133 66 1.0 1 57 9 134 47 1.0 1 38 9 135 58 1.0 1 47 11 136 47 1.0 1 33 14 137 58 1.0 1 55 3 138 38 1.0 1 30 8 139 51 1.0 1 43 8 140 35 1.0 1 30 5 141 35 1.0 1 24 11 142 24 1.0 1 15 9 143 43 1.0 1 28 15 144 21 1.0 1 15 6 145 20 1.0 1 14 6 146 26 1.0 1 13 13 147 29 1.0 1 23 6 148 31 1.0 1 18 13 149 45 1.0 1 33 12 150 17 1.0 1 11 6 151 75 1.0 1 21 54 RUN STATISTICS FOR INPUT FILE: ERR12308516_2.fastq.gz ============================================= 65523131 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 65523131 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27400 (0.04%)