SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308505_1.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: 137361). 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 ERR12308505_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1130.047 s (18.417 µs/read; 3.26 M reads/minute). === Summary === Total reads processed: 61,359,468 Reads with adapters: 34,846,583 (56.8%) Reads written (passing filters): 61,359,468 (100.0%) Total basepairs processed: 9,265,279,668 bp Quality-trimmed: 51,351,547 bp (0.6%) Total written (filtered): 8,837,726,131 bp (95.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34846583 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.5% C: 19.7% G: 2.0% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 23107032 15339867.0 0 23107032 2 572786 3834966.8 0 572786 3 361522 958741.7 0 361522 4 271443 239685.4 0 271443 5 282793 59921.4 0 282793 6 248074 14980.3 0 248074 7 242533 3745.1 0 242533 8 294709 936.3 0 294709 9 157429 234.1 0 156994 435 10 252222 58.5 1 223290 28932 11 221544 14.6 1 197942 23602 12 237765 3.7 1 198433 39332 13 231861 0.9 1 192580 39281 14 267560 0.9 1 218372 49188 15 194302 0.9 1 163377 30925 16 220006 0.9 1 184038 35968 17 283848 0.9 1 239842 44006 18 146790 0.9 1 122516 24274 19 264901 0.9 1 219934 44967 20 218683 0.9 1 183778 34905 21 136779 0.9 1 115016 21763 22 196626 0.9 1 164471 32155 23 195411 0.9 1 163441 31970 24 259280 0.9 1 214564 44716 25 231206 0.9 1 195144 36062 26 141151 0.9 1 118086 23065 27 129918 0.9 1 109033 20885 28 206829 0.9 1 176160 30669 29 148844 0.9 1 126974 21870 30 201047 0.9 1 170271 30776 31 135527 0.9 1 114558 20969 32 177228 0.9 1 148954 28274 33 158302 0.9 1 134064 24238 34 145198 0.9 1 124090 21108 35 193383 0.9 1 165487 27896 36 151456 0.9 1 129961 21495 37 122388 0.9 1 105691 16697 38 137384 0.9 1 117860 19524 39 132166 0.9 1 113547 18619 40 128676 0.9 1 111521 17155 41 130580 0.9 1 113122 17458 42 144767 0.9 1 124790 19977 43 108621 0.9 1 93474 15147 44 123019 0.9 1 105435 17584 45 130196 0.9 1 111488 18708 46 116298 0.9 1 100439 15859 47 115242 0.9 1 100619 14623 48 103903 0.9 1 90202 13701 49 110353 0.9 1 95601 14752 50 101802 0.9 1 89196 12606 51 98419 0.9 1 86056 12363 52 98142 0.9 1 85622 12520 53 93361 0.9 1 82013 11348 54 107839 0.9 1 94942 12897 55 71840 0.9 1 63187 8653 56 89186 0.9 1 78054 11132 57 114569 0.9 1 100771 13798 58 62664 0.9 1 54941 7723 59 71258 0.9 1 63275 7983 60 87325 0.9 1 77765 9560 61 78498 0.9 1 69609 8889 62 59177 0.9 1 52632 6545 63 122572 0.9 1 109459 13113 64 56081 0.9 1 49766 6315 65 43285 0.9 1 38415 4870 66 42804 0.9 1 38192 4612 67 67157 0.9 1 60609 6548 68 58987 0.9 1 52956 6031 69 50064 0.9 1 45053 5011 70 54958 0.9 1 49841 5117 71 49931 0.9 1 45193 4738 72 49539 0.9 1 44765 4774 73 63376 0.9 1 57770 5606 74 46335 0.9 1 42192 4143 75 45877 0.9 1 42083 3794 76 26226 0.9 1 23903 2323 77 25043 0.9 1 22635 2408 78 26997 0.9 1 24584 2413 79 26255 0.9 1 23929 2326 80 25655 0.9 1 23458 2197 81 24532 0.9 1 22392 2140 82 23534 0.9 1 21565 1969 83 23038 0.9 1 21181 1857 84 21560 0.9 1 19723 1837 85 20884 0.9 1 19116 1768 86 18637 0.9 1 17159 1478 87 17341 0.9 1 15969 1372 88 16169 0.9 1 14955 1214 89 15525 0.9 1 14397 1128 90 14354 0.9 1 13300 1054 91 13304 0.9 1 12296 1008 92 12369 0.9 1 11496 873 93 11868 0.9 1 10962 906 94 10282 0.9 1 9581 701 95 9782 0.9 1 9063 719 96 9054 0.9 1 8406 648 97 8359 0.9 1 7757 602 98 7906 0.9 1 7355 551 99 7444 0.9 1 6953 491 100 6842 0.9 1 6400 442 101 5821 0.9 1 5458 363 102 5036 0.9 1 4651 385 103 4400 0.9 1 4097 303 104 4116 0.9 1 3824 292 105 3721 0.9 1 3466 255 106 3230 0.9 1 3037 193 107 2904 0.9 1 2725 179 108 2591 0.9 1 2434 157 109 2256 0.9 1 2120 136 110 1987 0.9 1 1893 94 111 1740 0.9 1 1629 111 112 1491 0.9 1 1395 96 113 1306 0.9 1 1218 88 114 1087 0.9 1 1008 79 115 945 0.9 1 886 59 116 710 0.9 1 658 52 117 653 0.9 1 616 37 118 546 0.9 1 490 56 119 503 0.9 1 456 47 120 466 0.9 1 419 47 121 396 0.9 1 355 41 122 309 0.9 1 260 49 123 269 0.9 1 241 28 124 219 0.9 1 184 35 125 230 0.9 1 186 44 126 219 0.9 1 193 26 127 184 0.9 1 163 21 128 158 0.9 1 138 20 129 131 0.9 1 118 13 130 127 0.9 1 107 20 131 131 0.9 1 121 10 132 88 0.9 1 77 11 133 91 0.9 1 75 16 134 87 0.9 1 80 7 135 112 0.9 1 96 16 136 61 0.9 1 58 3 137 59 0.9 1 53 6 138 43 0.9 1 37 6 139 63 0.9 1 51 12 140 56 0.9 1 53 3 141 53 0.9 1 47 6 142 47 0.9 1 42 5 143 46 0.9 1 34 12 144 45 0.9 1 32 13 145 35 0.9 1 31 4 146 33 0.9 1 19 14 147 38 0.9 1 27 11 148 26 0.9 1 22 4 149 52 0.9 1 36 16 150 29 0.9 1 16 13 151 50 0.9 1 19 31 RUN STATISTICS FOR INPUT FILE: ERR12308505_1.fastq.gz ============================================= 61359468 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 61359468 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23749 (0.04%)