SUMMARISING RUN PARAMETERS ========================== Input filename: DE-3_trimmed_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.9 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 2438). Second best hit was smallRNA (count: 8) 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: -t 12 Output file will be GZIP compressed This is cutadapt 4.9 with Python 3.12.8 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC DE-3_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 343.422 s (4.131 µs/read; 14.52 M reads/minute). === Summary === Total reads processed: 83,123,897 Reads with adapters: 21,949,625 (26.4%) Reads written (passing filters): 83,123,897 (100.0%) Total basepairs processed: 11,808,460,334 bp Quality-trimmed: 153,497,991 bp (1.3%) Total written (filtered): 11,371,339,387 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21949625 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.4% C: 33.9% G: 29.2% T: 11.3% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9035554 20780974.2 0 9035554 2 4368119 5195243.6 0 4368119 3 819332 1298810.9 0 819332 4 93078 324702.7 0 93078 5 31790 81175.7 0 31790 6 8524 20293.9 0 8524 7 5129 5073.5 0 5129 8 2401 1268.4 0 2401 9 13302 317.1 0 9453 3849 10 7868 79.3 1 4110 3758 11 12999 19.8 1 5893 7106 12 18635 5.0 1 9982 8653 13 8953 1.2 1 3310 5643 14 14141 1.2 1 6069 8072 15 20290 1.2 1 9707 10583 16 19398 1.2 1 9138 10260 17 29489 1.2 1 17687 11802 18 38823 1.2 1 21359 17464 19 152095 1.2 1 115480 36615 20 56646 1.2 1 42194 14452 21 21995 1.2 1 12333 9662 22 27534 1.2 1 14548 12986 23 49359 1.2 1 27455 21904 24 564630 1.2 1 504140 60490 25 204572 1.2 1 173825 30747 26 234898 1.2 1 205571 29327 27 1416195 1.2 1 1356205 59990 28 172524 1.2 1 154493 18031 29 548281 1.2 1 524561 23720 30 108803 1.2 1 100686 8117 31 64685 1.2 1 56585 8100 32 324424 1.2 1 306972 17452 33 138044 1.2 1 120910 17134 34 852180 1.2 1 819343 32837 35 182294 1.2 1 165726 16568 36 520448 1.2 1 496129 24319 37 59038 1.2 1 51756 7282 38 94912 1.2 1 89599 5313 39 28598 1.2 1 24704 3894 40 114472 1.2 1 103958 10514 41 250047 1.2 1 235479 14568 42 44607 1.2 1 38782 5825 43 46779 1.2 1 41591 5188 44 40337 1.2 1 33069 7268 45 130983 1.2 1 121960 9023 46 41054 1.2 1 37128 3926 47 28578 1.2 1 25302 3276 48 6218 1.2 1 4926 1292 49 26780 1.2 1 24065 2715 50 79137 1.2 1 74758 4379 51 21002 1.2 1 17885 3117 52 46052 1.2 1 43122 2930 53 39260 1.2 1 36171 3089 54 17750 1.2 1 15345 2405 55 54539 1.2 1 51726 2813 56 18550 1.2 1 16465 2085 57 22863 1.2 1 20935 1928 58 24744 1.2 1 22609 2135 59 49755 1.2 1 46430 3325 60 27353 1.2 1 25128 2225 61 19853 1.2 1 17632 2221 62 40803 1.2 1 38688 2115 63 13338 1.2 1 11682 1656 64 25181 1.2 1 23568 1613 65 15057 1.2 1 13716 1341 66 15088 1.2 1 13701 1387 67 18274 1.2 1 16807 1467 68 29625 1.2 1 27957 1668 69 23355 1.2 1 21779 1576 70 13261 1.2 1 12098 1163 71 25003 1.2 1 23809 1194 72 13540 1.2 1 12444 1096 73 13610 1.2 1 12730 880 74 16378 1.2 1 15553 825 75 16231 1.2 1 15575 656 76 6670 1.2 1 6269 401 77 1666 1.2 1 1388 278 78 2281 1.2 1 2025 256 79 4079 1.2 1 3768 311 80 5417 1.2 1 5078 339 81 5774 1.2 1 5429 345 82 5710 1.2 1 5310 400 83 5573 1.2 1 5168 405 84 5286 1.2 1 4915 371 85 4597 1.2 1 4247 350 86 4338 1.2 1 4017 321 87 3880 1.2 1 3558 322 88 3683 1.2 1 3395 288 89 3440 1.2 1 3177 263 90 3211 1.2 1 2965 246 91 3023 1.2 1 2802 221 92 2840 1.2 1 2622 218 93 2640 1.2 1 2426 214 94 2447 1.2 1 2187 260 95 2288 1.2 1 2122 166 96 2087 1.2 1 1919 168 97 1960 1.2 1 1795 165 98 1666 1.2 1 1558 108 99 1625 1.2 1 1444 181 100 1514 1.2 1 1385 129 101 1407 1.2 1 1275 132 102 1391 1.2 1 1220 171 103 1207 1.2 1 1098 109 104 1167 1.2 1 1043 124 105 1046 1.2 1 933 113 106 929 1.2 1 831 98 107 923 1.2 1 825 98 108 885 1.2 1 765 120 109 929 1.2 1 769 160 110 711 1.2 1 614 97 111 693 1.2 1 596 97 112 722 1.2 1 571 151 113 635 1.2 1 503 132 114 599 1.2 1 516 83 115 603 1.2 1 497 106 116 552 1.2 1 473 79 117 525 1.2 1 444 81 118 653 1.2 1 486 167 119 504 1.2 1 430 74 120 524 1.2 1 435 89 121 494 1.2 1 424 70 122 504 1.2 1 414 90 123 548 1.2 1 445 103 124 514 1.2 1 444 70 125 579 1.2 1 489 90 126 599 1.2 1 508 91 127 603 1.2 1 543 60 128 674 1.2 1 587 87 129 846 1.2 1 739 107 130 790 1.2 1 716 74 131 869 1.2 1 761 108 132 1045 1.2 1 920 125 133 1220 1.2 1 1075 145 134 1519 1.2 1 1399 120 135 1574 1.2 1 1432 142 136 1495 1.2 1 1372 123 137 1825 1.2 1 1675 150 138 1956 1.2 1 1806 150 139 1825 1.2 1 1685 140 140 2163 1.2 1 1992 171 141 3324 1.2 1 3083 241 142 1793 1.2 1 1608 185 143 2108 1.2 1 1958 150 144 2443 1.2 1 2304 139 145 2680 1.2 1 2511 169 146 4311 1.2 1 4060 251 147 5231 1.2 1 4899 332 148 1310 1.2 1 1188 122 149 222 1.2 1 63 159 150 824 1.2 1 465 359 RUN STATISTICS FOR INPUT FILE: DE-3_trimmed_2.fastq.gz ============================================= 83123897 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 83123897 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 658116 (0.79%)