SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684009_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: 121147). Second best hit was Nextera (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 ERR10684009_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 2278.270 s (17.329 µs/read; 3.46 M reads/minute). === Summary === Total reads processed: 131,474,544 Reads with adapters: 76,672,661 (58.3%) Reads written (passing filters): 131,474,544 (100.0%) Total basepairs processed: 19,852,656,144 bp Quality-trimmed: 74,627,957 bp (0.4%) Total written (filtered): 18,959,448,584 bp (95.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 76672661 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.3% C: 17.2% G: 0.5% T: 31.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 56421526 32868636.0 0 56421526 2 412630 8217159.0 0 412630 3 413692 2054289.8 0 413692 4 347597 513572.4 0 347597 5 364846 128393.1 0 364846 6 322575 32098.3 0 322575 7 314895 8024.6 0 314895 8 397781 2006.1 0 397781 9 246439 501.5 0 245619 820 10 349041 125.4 1 322239 26802 11 298123 31.3 1 269875 28248 12 344141 7.8 1 299908 44233 13 326028 2.0 1 285331 40697 14 383200 2.0 1 335023 48177 15 268270 2.0 1 234005 34265 16 312004 2.0 1 272706 39298 17 415022 2.0 1 366620 48402 18 198417 2.0 1 173100 25317 19 405360 2.0 1 356186 49174 20 316271 2.0 1 279607 36664 21 208107 2.0 1 181886 26221 22 300614 2.0 1 264896 35718 23 303731 2.0 1 267635 36096 24 393025 2.0 1 347142 45883 25 350519 2.0 1 311668 38851 26 252103 2.0 1 222719 29384 27 209622 2.0 1 183235 26387 28 344952 2.0 1 309645 35307 29 215186 2.0 1 189225 25961 30 342948 2.0 1 308024 34924 31 213534 2.0 1 188902 24632 32 311903 2.0 1 278742 33161 33 278720 2.0 1 248662 30058 34 231019 2.0 1 207094 23925 35 342364 2.0 1 308908 33456 36 259454 2.0 1 233132 26322 37 214999 2.0 1 193329 21670 38 252261 2.0 1 226436 25825 39 247093 2.0 1 221035 26058 40 213791 2.0 1 193399 20392 41 243753 2.0 1 219585 24168 42 289626 2.0 1 261581 28045 43 196210 2.0 1 176089 20121 44 233562 2.0 1 211703 21859 45 253764 2.0 1 229141 24623 46 237780 2.0 1 214945 22835 47 227487 2.0 1 207981 19506 48 195297 2.0 1 176431 18866 49 229593 2.0 1 207536 22057 50 199456 2.0 1 182872 16584 51 195590 2.0 1 178448 17142 52 202430 2.0 1 184481 17949 53 199922 2.0 1 182505 17417 54 246631 2.0 1 226487 20144 55 140025 2.0 1 127097 12928 56 195613 2.0 1 177944 17669 57 277023 2.0 1 254390 22633 58 126184 2.0 1 114583 11601 59 144763 2.0 1 132705 12058 60 213270 2.0 1 196393 16877 61 175226 2.0 1 160861 14365 62 126646 2.0 1 115500 11146 63 336755 2.0 1 313318 23437 64 125060 2.0 1 114375 10685 65 100428 2.0 1 92076 8352 66 99147 2.0 1 91060 8087 67 168157 2.0 1 156549 11608 68 144907 2.0 1 133629 11278 69 131031 2.0 1 121363 9668 70 151327 2.0 1 140610 10717 71 139977 2.0 1 129755 10222 72 138379 2.0 1 128139 10240 73 180495 2.0 1 168148 12347 74 111283 2.0 1 103543 7740 75 108948 2.0 1 101638 7310 76 79371 2.0 1 73819 5552 77 78473 2.0 1 72756 5717 78 83241 2.0 1 77656 5585 79 82295 2.0 1 76690 5605 80 81402 2.0 1 76043 5359 81 80159 2.0 1 74655 5504 82 79234 2.0 1 73892 5342 83 80417 2.0 1 75140 5277 84 76313 2.0 1 71339 4974 85 75974 2.0 1 71028 4946 86 70324 2.0 1 65878 4446 87 66212 2.0 1 62105 4107 88 62316 2.0 1 58424 3892 89 60379 2.0 1 56690 3689 90 59325 2.0 1 55920 3405 91 55020 2.0 1 51683 3337 92 52584 2.0 1 49432 3152 93 50488 2.0 1 47602 2886 94 46603 2.0 1 43837 2766 95 44898 2.0 1 42392 2506 96 42736 2.0 1 40359 2377 97 40298 2.0 1 37987 2311 98 39074 2.0 1 37023 2051 99 37791 2.0 1 35782 2009 100 35804 2.0 1 33865 1939 101 30896 2.0 1 29255 1641 102 28192 2.0 1 26785 1407 103 25655 2.0 1 24332 1323 104 23178 2.0 1 21977 1201 105 22104 2.0 1 21030 1074 106 19837 2.0 1 18871 966 107 18269 2.0 1 17394 875 108 16432 2.0 1 15596 836 109 14349 2.0 1 13657 692 110 13003 2.0 1 12406 597 111 11468 2.0 1 10929 539 112 9990 2.0 1 9553 437 113 8820 2.0 1 8414 406 114 7507 2.0 1 7176 331 115 6299 2.0 1 6024 275 116 4870 2.0 1 4671 199 117 3902 2.0 1 3721 181 118 3280 2.0 1 3142 138 119 2567 2.0 1 2460 107 120 5956 2.0 1 5649 307 121 1715 2.0 1 1644 71 122 1083 2.0 1 1021 62 123 773 2.0 1 732 41 124 505 2.0 1 469 36 125 325 2.0 1 312 13 126 274 2.0 1 255 19 127 155 2.0 1 141 14 128 131 2.0 1 113 18 129 82 2.0 1 71 11 130 69 2.0 1 60 9 131 56 2.0 1 50 6 132 58 2.0 1 51 7 133 51 2.0 1 50 1 134 40 2.0 1 35 5 135 43 2.0 1 39 4 136 20 2.0 1 20 137 44 2.0 1 41 3 138 29 2.0 1 25 4 139 29 2.0 1 27 2 140 24 2.0 1 19 5 141 39 2.0 1 33 6 142 35 2.0 1 23 12 143 20 2.0 1 12 8 144 15 2.0 1 6 9 145 32 2.0 1 21 11 146 5 2.0 1 3 2 147 22 2.0 1 15 7 148 17 2.0 1 5 12 149 20 2.0 1 13 7 150 14 2.0 1 5 9 151 83 2.0 1 56 27 RUN STATISTICS FOR INPUT FILE: ERR10684009_2.fastq.gz ============================================= 131474544 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 131474544 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 61015 (0.05%)