SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308515_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: 138362). 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 ERR12308515_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1357.054 s (18.522 µs/read; 3.24 M reads/minute). === Summary === Total reads processed: 73,268,862 Reads with adapters: 41,376,979 (56.5%) Reads written (passing filters): 73,268,862 (100.0%) Total basepairs processed: 11,063,598,162 bp Quality-trimmed: 60,535,110 bp (0.5%) Total written (filtered): 10,545,359,281 bp (95.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 41376979 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.9% C: 19.0% G: 2.4% T: 28.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 27060811 18317215.5 0 27060811 2 778461 4579303.9 0 778461 3 448058 1144826.0 0 448058 4 314436 286206.5 0 314436 5 334433 71551.6 0 334433 6 295610 17887.9 0 295610 7 276998 4472.0 0 276998 8 327521 1118.0 0 327521 9 217982 279.5 0 217495 487 10 293510 69.9 1 262295 31215 11 270076 17.5 1 240487 29589 12 289913 4.4 1 252088 37825 13 274385 1.1 1 240743 33642 14 322424 1.1 1 278221 44203 15 228193 1.1 1 200793 27400 16 262536 1.1 1 230293 32243 17 335330 1.1 1 296714 38616 18 174571 1.1 1 152896 21675 19 320096 1.1 1 279655 40441 20 272217 1.1 1 240529 31688 21 156676 1.1 1 137872 18804 22 240660 1.1 1 211495 29165 23 238776 1.1 1 209103 29673 24 292280 1.1 1 253677 38603 25 265762 1.1 1 235401 30361 26 185565 1.1 1 162669 22896 27 184807 1.1 1 161838 22969 28 239073 1.1 1 213511 25562 29 189163 1.1 1 168794 20369 30 227498 1.1 1 202265 25233 31 189428 1.1 1 168958 20470 32 208427 1.1 1 185503 22924 33 229482 1.1 1 204369 25113 34 162075 1.1 1 145324 16751 35 200419 1.1 1 178319 22100 36 187168 1.1 1 169520 17648 37 172762 1.1 1 155273 17489 38 173336 1.1 1 155846 17490 39 182747 1.1 1 164281 18466 40 203590 1.1 1 185003 18587 41 121155 1.1 1 109067 12088 42 175730 1.1 1 159105 16625 43 139861 1.1 1 125729 14132 44 158201 1.1 1 142222 15979 45 163923 1.1 1 147561 16362 46 137756 1.1 1 123952 13804 47 143566 1.1 1 130974 12592 48 133547 1.1 1 121300 12247 49 131185 1.1 1 118637 12548 50 125088 1.1 1 114803 10285 51 121248 1.1 1 110727 10521 52 120710 1.1 1 110233 10477 53 116858 1.1 1 106881 9977 54 144752 1.1 1 133032 11720 55 77535 1.1 1 70761 6774 56 109017 1.1 1 99393 9624 57 129639 1.1 1 118157 11482 58 78485 1.1 1 71646 6839 59 89272 1.1 1 82369 6903 60 95532 1.1 1 88066 7466 61 93073 1.1 1 85661 7412 62 81293 1.1 1 74576 6717 63 138108 1.1 1 127864 10244 64 75699 1.1 1 70033 5666 65 53316 1.1 1 49197 4119 66 51070 1.1 1 47118 3952 67 79624 1.1 1 74339 5285 68 70028 1.1 1 65067 4961 69 58898 1.1 1 54664 4234 70 63897 1.1 1 59755 4142 71 58482 1.1 1 54538 3944 72 57601 1.1 1 53744 3857 73 75119 1.1 1 70350 4769 74 53403 1.1 1 49745 3658 75 53215 1.1 1 49756 3459 76 29887 1.1 1 27759 2128 77 28692 1.1 1 26779 1913 78 30849 1.1 1 28869 1980 79 30670 1.1 1 28730 1940 80 29738 1.1 1 27895 1843 81 28391 1.1 1 26591 1800 82 27239 1.1 1 25494 1745 83 26765 1.1 1 25050 1715 84 24691 1.1 1 23149 1542 85 24092 1.1 1 22608 1484 86 22033 1.1 1 20675 1358 87 20016 1.1 1 18865 1151 88 18919 1.1 1 17767 1152 89 17823 1.1 1 16800 1023 90 17636 1.1 1 16635 1001 91 16124 1.1 1 15185 939 92 14889 1.1 1 14075 814 93 14033 1.1 1 13237 796 94 12763 1.1 1 12002 761 95 12014 1.1 1 11336 678 96 11092 1.1 1 10519 573 97 10329 1.1 1 9787 542 98 9986 1.1 1 9447 539 99 9448 1.1 1 8945 503 100 9108 1.1 1 8580 528 101 7741 1.1 1 7288 453 102 6953 1.1 1 6567 386 103 6265 1.1 1 5938 327 104 5747 1.1 1 5423 324 105 5277 1.1 1 4982 295 106 4951 1.1 1 4651 300 107 4485 1.1 1 4217 268 108 4197 1.1 1 3985 212 109 3689 1.1 1 3496 193 110 3369 1.1 1 3170 199 111 2974 1.1 1 2799 175 112 2676 1.1 1 2531 145 113 2246 1.1 1 2109 137 114 1948 1.1 1 1836 112 115 1844 1.1 1 1745 99 116 1568 1.1 1 1491 77 117 1349 1.1 1 1256 93 118 1185 1.1 1 1107 78 119 1047 1.1 1 977 70 120 1221 1.1 1 1153 68 121 935 1.1 1 867 68 122 655 1.1 1 593 62 123 543 1.1 1 482 61 124 434 1.1 1 392 42 125 424 1.1 1 364 60 126 306 1.1 1 269 37 127 268 1.1 1 230 38 128 215 1.1 1 184 31 129 186 1.1 1 153 33 130 161 1.1 1 133 28 131 146 1.1 1 127 19 132 122 1.1 1 94 28 133 113 1.1 1 88 25 134 80 1.1 1 62 18 135 88 1.1 1 79 9 136 72 1.1 1 59 13 137 85 1.1 1 66 19 138 63 1.1 1 58 5 139 78 1.1 1 58 20 140 49 1.1 1 34 15 141 71 1.1 1 56 15 142 55 1.1 1 38 17 143 40 1.1 1 28 12 144 47 1.1 1 34 13 145 55 1.1 1 41 14 146 53 1.1 1 36 17 147 69 1.1 1 41 28 148 47 1.1 1 23 24 149 50 1.1 1 38 12 150 42 1.1 1 23 19 151 327 1.1 1 67 260 RUN STATISTICS FOR INPUT FILE: ERR12308515_1.fastq.gz ============================================= 73268862 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 73268862 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 58509 (0.08%)