SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308510_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: 106891). Second best hit was Nextera (count: 1) 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 ERR12308510_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1283.706 s (17.475 µs/read; 3.43 M reads/minute). === Summary === Total reads processed: 73,458,386 Reads with adapters: 40,362,951 (54.9%) Reads written (passing filters): 73,458,386 (100.0%) Total basepairs processed: 11,092,216,286 bp Quality-trimmed: 60,005,949 bp (0.5%) Total written (filtered): 10,671,743,812 bp (96.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40362951 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.3% C: 18.4% G: 1.5% T: 29.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29158009 18364596.5 0 29158009 2 614410 4591149.1 0 614410 3 364301 1147787.3 0 364301 4 276063 286946.8 0 276063 5 284507 71736.7 0 284507 6 246527 17934.2 0 246527 7 239016 4483.5 0 239016 8 294247 1120.9 0 294247 9 146766 280.2 0 146248 518 10 251783 70.1 1 217571 34212 11 208709 17.5 1 183115 25594 12 234130 4.4 1 197884 36246 13 220663 1.1 1 188225 32438 14 262831 1.1 1 219427 43404 15 181239 1.1 1 155242 25997 16 208024 1.1 1 178020 30004 17 272409 1.1 1 235391 37018 18 133992 1.1 1 114513 19479 19 266942 1.1 1 225980 40962 20 204652 1.1 1 176719 27933 21 113859 1.1 1 98167 15692 22 184803 1.1 1 158404 26399 23 182110 1.1 1 155635 26475 24 228088 1.1 1 192073 36015 25 209619 1.1 1 180973 28646 26 151223 1.1 1 129522 21701 27 119841 1.1 1 102623 17218 28 189745 1.1 1 164806 24939 29 137241 1.1 1 120122 17119 30 192328 1.1 1 166163 26165 31 119603 1.1 1 103827 15776 32 186055 1.1 1 160229 25826 33 159058 1.1 1 138902 20156 34 101152 1.1 1 88632 12520 35 153884 1.1 1 135620 18264 36 142717 1.1 1 125248 17469 37 140255 1.1 1 125100 15155 38 98334 1.1 1 86469 11865 39 162634 1.1 1 143883 18751 40 91924 1.1 1 80854 11070 41 127562 1.1 1 112539 15023 42 130041 1.1 1 114883 15158 43 102506 1.1 1 90700 11806 44 114787 1.1 1 101119 13668 45 122097 1.1 1 107259 14838 46 107242 1.1 1 94804 12438 47 105975 1.1 1 94691 11284 48 95426 1.1 1 85015 10411 49 102354 1.1 1 90745 11609 50 95279 1.1 1 85531 9748 51 92343 1.1 1 82862 9481 52 92809 1.1 1 82950 9859 53 87933 1.1 1 79161 8772 54 100269 1.1 1 90363 9906 55 68205 1.1 1 61792 6413 56 84096 1.1 1 75374 8722 57 108286 1.1 1 96925 11361 58 58537 1.1 1 52472 6065 59 65404 1.1 1 59605 5799 60 81788 1.1 1 74190 7598 61 74203 1.1 1 67509 6694 62 55933 1.1 1 50791 5142 63 114055 1.1 1 103762 10293 64 53592 1.1 1 48743 4849 65 41804 1.1 1 38116 3688 66 40769 1.1 1 37105 3664 67 63681 1.1 1 58598 5083 68 55609 1.1 1 50923 4686 69 48151 1.1 1 44101 4050 70 53330 1.1 1 49133 4197 71 48522 1.1 1 44804 3718 72 46768 1.1 1 43080 3688 73 60686 1.1 1 56466 4220 74 43418 1.1 1 40123 3295 75 44340 1.1 1 41224 3116 76 25579 1.1 1 23594 1985 77 23784 1.1 1 21932 1852 78 25290 1.1 1 23392 1898 79 24618 1.1 1 22843 1775 80 24608 1.1 1 22861 1747 81 23460 1.1 1 21725 1735 82 22262 1.1 1 20694 1568 83 21606 1.1 1 20056 1550 84 20221 1.1 1 18787 1434 85 19591 1.1 1 18102 1489 86 17712 1.1 1 16449 1263 87 16533 1.1 1 15390 1143 88 15229 1.1 1 14235 994 89 14346 1.1 1 13323 1023 90 13974 1.1 1 13081 893 91 12326 1.1 1 11494 832 92 11580 1.1 1 10853 727 93 10847 1.1 1 10222 625 94 9624 1.1 1 8971 653 95 9024 1.1 1 8468 556 96 8041 1.1 1 7552 489 97 7581 1.1 1 7093 488 98 7180 1.1 1 6724 456 99 6586 1.1 1 6180 406 100 6067 1.1 1 5705 362 101 5170 1.1 1 4834 336 102 4674 1.1 1 4370 304 103 3867 1.1 1 3632 235 104 3456 1.1 1 3263 193 105 3139 1.1 1 2944 195 106 2768 1.1 1 2616 152 107 2595 1.1 1 2433 162 108 2276 1.1 1 2122 154 109 2004 1.1 1 1880 124 110 1643 1.1 1 1544 99 111 1485 1.1 1 1398 87 112 1267 1.1 1 1196 71 113 1222 1.1 1 1144 78 114 900 1.1 1 840 60 115 788 1.1 1 722 66 116 573 1.1 1 522 51 117 533 1.1 1 499 34 118 453 1.1 1 418 35 119 435 1.1 1 384 51 120 546 1.1 1 488 58 121 575 1.1 1 536 39 122 326 1.1 1 286 40 123 226 1.1 1 193 33 124 203 1.1 1 175 28 125 188 1.1 1 170 18 126 166 1.1 1 140 26 127 179 1.1 1 145 34 128 159 1.1 1 133 26 129 154 1.1 1 130 24 130 112 1.1 1 95 17 131 153 1.1 1 135 18 132 79 1.1 1 65 14 133 108 1.1 1 98 10 134 69 1.1 1 60 9 135 97 1.1 1 81 16 136 73 1.1 1 57 16 137 109 1.1 1 90 19 138 56 1.1 1 44 12 139 70 1.1 1 63 7 140 64 1.1 1 51 13 141 69 1.1 1 60 9 142 46 1.1 1 40 6 143 53 1.1 1 38 15 144 45 1.1 1 27 18 145 53 1.1 1 38 15 146 62 1.1 1 41 21 147 63 1.1 1 41 22 148 46 1.1 1 30 16 149 71 1.1 1 52 19 150 58 1.1 1 31 27 151 263 1.1 1 67 196 RUN STATISTICS FOR INPUT FILE: ERR12308510_2.fastq.gz ============================================= 73458386 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 73458386 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 52709 (0.07%)