SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684008_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: 225983). 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 ERR10684008_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1441.987 s (15.522 µs/read; 3.87 M reads/minute). === Summary === Total reads processed: 92,899,213 Reads with adapters: 62,071,115 (66.8%) Reads written (passing filters): 92,899,213 (100.0%) Total basepairs processed: 14,027,781,163 bp Quality-trimmed: 49,746,751 bp (0.4%) Total written (filtered): 13,052,853,149 bp (93.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62071115 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.3% C: 18.8% G: 0.8% T: 28.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 31313418 23224803.2 0 31313418 2 1163742 5806200.8 0 1163742 3 875743 1451550.2 0 875743 4 716340 362887.6 0 716340 5 758445 90721.9 0 758445 6 740618 22680.5 0 740618 7 749160 5670.1 0 749160 8 881914 1417.5 0 881914 9 603150 354.4 0 601328 1822 10 753934 88.6 1 686672 67262 11 655529 22.1 1 603309 52220 12 683907 5.5 1 600783 83124 13 637143 1.4 1 559457 77686 14 751329 1.4 1 654680 96649 15 488412 1.4 1 432547 55865 16 617487 1.4 1 549396 68091 17 844998 1.4 1 748675 96323 18 424635 1.4 1 375993 48642 19 791760 1.4 1 700352 91408 20 589434 1.4 1 524242 65192 21 404672 1.4 1 361969 42703 22 522470 1.4 1 466230 56240 23 505824 1.4 1 449832 55992 24 586769 1.4 1 513536 73233 25 560609 1.4 1 500453 60156 26 428532 1.4 1 382754 45778 27 393079 1.4 1 348726 44353 28 579298 1.4 1 517898 61400 29 463576 1.4 1 415643 47933 30 597017 1.4 1 535740 61277 31 396605 1.4 1 355858 40747 32 469712 1.4 1 418090 51622 33 405430 1.4 1 363127 42303 34 395315 1.4 1 357429 37886 35 306456 1.4 1 275727 30729 36 362369 1.4 1 326147 36222 37 350492 1.4 1 316730 33762 38 358608 1.4 1 325668 32940 39 437450 1.4 1 396873 40577 40 319517 1.4 1 290618 28899 41 352485 1.4 1 319313 33172 42 348993 1.4 1 316765 32228 43 256699 1.4 1 233175 23524 44 273968 1.4 1 248051 25917 45 276276 1.4 1 250171 26105 46 265831 1.4 1 242004 23827 47 256090 1.4 1 232261 23829 48 262919 1.4 1 239759 23160 49 282899 1.4 1 257992 24907 50 262160 1.4 1 240176 21984 51 242950 1.4 1 222503 20447 52 230657 1.4 1 211640 19017 53 214137 1.4 1 195578 18559 54 233836 1.4 1 213629 20207 55 153942 1.4 1 141143 12799 56 189488 1.4 1 173118 16370 57 254283 1.4 1 232865 21418 58 136496 1.4 1 124223 12273 59 188267 1.4 1 173723 14544 60 221081 1.4 1 202812 18269 61 200936 1.4 1 185686 15250 62 158634 1.4 1 146062 12572 63 232263 1.4 1 214711 17552 64 116188 1.4 1 106639 9549 65 121972 1.4 1 113010 8962 66 90867 1.4 1 83783 7084 67 134755 1.4 1 124838 9917 68 133176 1.4 1 123396 9780 69 124334 1.4 1 115144 9190 70 134928 1.4 1 125196 9732 71 132565 1.4 1 122939 9626 72 126290 1.4 1 117118 9172 73 145482 1.4 1 135420 10062 74 113895 1.4 1 106025 7870 75 99769 1.4 1 93276 6493 76 63525 1.4 1 59184 4341 77 61080 1.4 1 56698 4382 78 65119 1.4 1 60634 4485 79 65211 1.4 1 60699 4512 80 67156 1.4 1 62584 4572 81 67693 1.4 1 63093 4600 82 62291 1.4 1 58080 4211 83 56268 1.4 1 52554 3714 84 50983 1.4 1 47732 3251 85 49151 1.4 1 45922 3229 86 44768 1.4 1 41942 2826 87 41986 1.4 1 39246 2740 88 39544 1.4 1 36928 2616 89 39174 1.4 1 36775 2399 90 38793 1.4 1 36493 2300 91 36773 1.4 1 34534 2239 92 34977 1.4 1 32918 2059 93 32277 1.4 1 30405 1872 94 27893 1.4 1 26271 1622 95 25138 1.4 1 23641 1497 96 23276 1.4 1 21932 1344 97 21112 1.4 1 19864 1248 98 20034 1.4 1 18820 1214 99 19422 1.4 1 18271 1151 100 18597 1.4 1 17531 1066 101 16748 1.4 1 15832 916 102 15192 1.4 1 14381 811 103 14031 1.4 1 13241 790 104 12116 1.4 1 11483 633 105 10921 1.4 1 10289 632 106 9947 1.4 1 9421 526 107 8652 1.4 1 8171 481 108 7873 1.4 1 7487 386 109 7093 1.4 1 6733 360 110 6546 1.4 1 6197 349 111 5628 1.4 1 5340 288 112 5036 1.4 1 4786 250 113 4393 1.4 1 4180 213 114 3562 1.4 1 3415 147 115 3008 1.4 1 2873 135 116 2527 1.4 1 2411 116 117 2037 1.4 1 1943 94 118 1694 1.4 1 1601 93 119 1351 1.4 1 1303 48 120 1976 1.4 1 1903 73 121 992 1.4 1 939 53 122 702 1.4 1 665 37 123 441 1.4 1 412 29 124 349 1.4 1 335 14 125 240 1.4 1 221 19 126 201 1.4 1 186 15 127 139 1.4 1 120 19 128 98 1.4 1 93 5 129 73 1.4 1 67 6 130 51 1.4 1 42 9 131 52 1.4 1 40 12 132 48 1.4 1 39 9 133 55 1.4 1 46 9 134 32 1.4 1 24 8 135 30 1.4 1 24 6 136 24 1.4 1 15 9 137 32 1.4 1 24 8 138 33 1.4 1 21 12 139 35 1.4 1 27 8 140 23 1.4 1 14 9 141 27 1.4 1 18 9 142 25 1.4 1 11 14 143 27 1.4 1 12 15 144 39 1.4 1 7 32 145 41 1.4 1 18 23 146 32 1.4 1 7 25 147 31 1.4 1 16 15 148 35 1.4 1 11 24 149 32 1.4 1 15 17 150 27 1.4 1 7 20 151 168 1.4 1 121 47 RUN STATISTICS FOR INPUT FILE: ERR10684008_2.fastq.gz ============================================= 92899213 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 92899213 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 41615 (0.04%)