SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684011_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: 106087). 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 ERR10684011_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1231.087 s (17.179 µs/read; 3.49 M reads/minute). === Summary === Total reads processed: 71,661,379 Reads with adapters: 40,364,575 (56.3%) Reads written (passing filters): 71,661,379 (100.0%) Total basepairs processed: 10,820,868,229 bp Quality-trimmed: 49,421,479 bp (0.5%) Total written (filtered): 10,380,715,620 bp (95.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40364575 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.3% C: 18.9% G: 1.1% T: 29.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29570010 17915344.8 0 29570010 2 780015 4478836.2 0 780015 3 263706 1119709.0 0 263706 4 201408 279927.3 0 201408 5 207847 69981.8 0 207847 6 188616 17495.5 0 188616 7 190488 4373.9 0 190488 8 227075 1093.5 0 227075 9 135131 273.4 0 134291 840 10 200550 68.3 1 179998 20552 11 162545 17.1 1 144557 17988 12 187534 4.3 1 162028 25506 13 187475 1.1 1 162003 25472 14 219738 1.1 1 189652 30086 15 146788 1.1 1 127139 19649 16 171961 1.1 1 149306 22655 17 232854 1.1 1 203695 29159 18 107096 1.1 1 92729 14367 19 234998 1.1 1 204643 30355 20 164384 1.1 1 144661 19723 21 100240 1.1 1 87468 12772 22 160040 1.1 1 139697 20343 23 160543 1.1 1 140053 20490 24 218754 1.1 1 190780 27974 25 180399 1.1 1 159505 20894 26 128532 1.1 1 113019 15513 27 106112 1.1 1 92797 13315 28 172490 1.1 1 153617 18873 29 119865 1.1 1 105723 14142 30 146056 1.1 1 129876 16180 31 140211 1.1 1 124432 15779 32 143373 1.1 1 127659 15714 33 139361 1.1 1 123909 15452 34 146119 1.1 1 128995 17124 35 137780 1.1 1 124202 13578 36 139030 1.1 1 124888 14142 37 100887 1.1 1 89235 11652 38 130598 1.1 1 117038 13560 39 145918 1.1 1 130613 15305 40 104653 1.1 1 93670 10983 41 114659 1.1 1 103098 11561 42 136689 1.1 1 123221 13468 43 93329 1.1 1 84087 9242 44 115846 1.1 1 104611 11235 45 121089 1.1 1 109212 11877 46 110162 1.1 1 99498 10664 47 110801 1.1 1 100855 9946 48 97519 1.1 1 88139 9380 49 103961 1.1 1 93921 10040 50 97312 1.1 1 89038 8274 51 90170 1.1 1 82268 7902 52 93367 1.1 1 85082 8285 53 93599 1.1 1 85238 8361 54 118601 1.1 1 108790 9811 55 60058 1.1 1 54492 5566 56 90339 1.1 1 82125 8214 57 129741 1.1 1 118670 11071 58 57161 1.1 1 51772 5389 59 64376 1.1 1 58999 5377 60 95994 1.1 1 88048 7946 61 80366 1.1 1 73991 6375 62 56848 1.1 1 51830 5018 63 151718 1.1 1 140762 10956 64 56660 1.1 1 51871 4789 65 44647 1.1 1 41083 3564 66 42144 1.1 1 38602 3542 67 76223 1.1 1 71024 5199 68 64543 1.1 1 59725 4818 69 57974 1.1 1 53606 4368 70 65054 1.1 1 60589 4465 71 60985 1.1 1 56657 4328 72 60088 1.1 1 55721 4367 73 77412 1.1 1 72288 5124 74 46529 1.1 1 43249 3280 75 44825 1.1 1 41875 2950 76 31995 1.1 1 29728 2267 77 33526 1.1 1 31081 2445 78 36053 1.1 1 33546 2507 79 35458 1.1 1 33106 2352 80 34907 1.1 1 32612 2295 81 34127 1.1 1 31819 2308 82 33535 1.1 1 31288 2247 83 33511 1.1 1 31335 2176 84 31552 1.1 1 29574 1978 85 31087 1.1 1 29022 2065 86 28412 1.1 1 26638 1774 87 26854 1.1 1 25189 1665 88 25991 1.1 1 24369 1622 89 24651 1.1 1 23090 1561 90 24187 1.1 1 22746 1441 91 22315 1.1 1 20990 1325 92 21430 1.1 1 20181 1249 93 20516 1.1 1 19328 1188 94 18724 1.1 1 17619 1105 95 17959 1.1 1 16928 1031 96 17084 1.1 1 16118 966 97 16075 1.1 1 15150 925 98 15461 1.1 1 14601 860 99 14849 1.1 1 13985 864 100 14188 1.1 1 13340 848 101 12317 1.1 1 11610 707 102 11235 1.1 1 10626 609 103 10357 1.1 1 9813 544 104 9287 1.1 1 8764 523 105 8852 1.1 1 8382 470 106 8054 1.1 1 7670 384 107 7399 1.1 1 7018 381 108 6715 1.1 1 6370 345 109 5867 1.1 1 5556 311 110 5312 1.1 1 5042 270 111 4819 1.1 1 4567 252 112 4260 1.1 1 4036 224 113 3889 1.1 1 3714 175 114 3346 1.1 1 3189 157 115 2947 1.1 1 2805 142 116 2586 1.1 1 2463 123 117 2313 1.1 1 2178 135 118 2028 1.1 1 1939 89 119 1790 1.1 1 1693 97 120 15541 1.1 1 14776 765 121 2144 1.1 1 2047 97 122 1040 1.1 1 999 41 123 780 1.1 1 740 40 124 615 1.1 1 573 42 125 476 1.1 1 442 34 126 405 1.1 1 375 30 127 322 1.1 1 296 26 128 234 1.1 1 219 15 129 203 1.1 1 186 17 130 187 1.1 1 167 20 131 235 1.1 1 210 25 132 142 1.1 1 123 19 133 176 1.1 1 160 16 134 142 1.1 1 131 11 135 162 1.1 1 154 8 136 135 1.1 1 125 10 137 169 1.1 1 157 12 138 112 1.1 1 99 13 139 140 1.1 1 131 9 140 105 1.1 1 89 16 141 128 1.1 1 115 13 142 99 1.1 1 74 25 143 112 1.1 1 90 22 144 69 1.1 1 49 20 145 136 1.1 1 109 27 146 101 1.1 1 86 15 147 103 1.1 1 71 32 148 87 1.1 1 66 21 149 128 1.1 1 105 23 150 81 1.1 1 59 22 151 277 1.1 1 191 86 RUN STATISTICS FOR INPUT FILE: ERR10684011_2.fastq.gz ============================================= 71661379 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 71661379 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 106736 (0.15%)