SUMMARISING RUN PARAMETERS ========================== Input filename: DE-1_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: 2209). Second best hit was smallRNA (count: 26) 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-1_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 377.302 s (4.192 µs/read; 14.31 M reads/minute). === Summary === Total reads processed: 90,005,528 Reads with adapters: 25,236,150 (28.0%) Reads written (passing filters): 90,005,528 (100.0%) Total basepairs processed: 12,674,977,119 bp Quality-trimmed: 183,896,105 bp (1.5%) Total written (filtered): 12,132,082,511 bp (95.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25236150 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.7% C: 34.4% G: 30.2% T: 10.6% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9685674 22501382.0 0 9685674 2 4988145 5625345.5 0 4988145 3 880892 1406336.4 0 880892 4 96525 351584.1 0 96525 5 34042 87896.0 0 34042 6 9475 21974.0 0 9475 7 5973 5493.5 0 5973 8 3075 1373.4 0 3075 9 15543 343.3 0 11074 4469 10 9751 85.8 1 5315 4436 11 15173 21.5 1 7333 7840 12 22555 5.4 1 12373 10182 13 10276 1.3 1 4056 6220 14 17585 1.3 1 7981 9604 15 24984 1.3 1 12464 12520 16 22436 1.3 1 10989 11447 17 36414 1.3 1 22344 14070 18 46511 1.3 1 26302 20209 19 188183 1.3 1 144286 43897 20 69792 1.3 1 52544 17248 21 25961 1.3 1 14959 11002 22 32990 1.3 1 17999 14991 23 58494 1.3 1 33122 25372 24 688027 1.3 1 615160 72867 25 249863 1.3 1 211951 37912 26 280238 1.3 1 244542 35696 27 1770375 1.3 1 1696947 73428 28 212396 1.3 1 190252 22144 29 671287 1.3 1 642896 28391 30 139239 1.3 1 128939 10300 31 76828 1.3 1 67103 9725 32 396748 1.3 1 375329 21419 33 168819 1.3 1 147365 21454 34 1073656 1.3 1 1033252 40404 35 235881 1.3 1 214927 20954 36 631721 1.3 1 602274 29447 37 73245 1.3 1 64143 9102 38 112782 1.3 1 106327 6455 39 37047 1.3 1 31993 5054 40 138558 1.3 1 125227 13331 41 310933 1.3 1 293169 17764 42 53563 1.3 1 46166 7397 43 59313 1.3 1 52794 6519 44 51983 1.3 1 42540 9443 45 170523 1.3 1 158917 11606 46 53907 1.3 1 48658 5249 47 36493 1.3 1 32157 4336 48 8030 1.3 1 6341 1689 49 37328 1.3 1 33688 3640 50 102222 1.3 1 96501 5721 51 27107 1.3 1 22965 4142 52 60076 1.3 1 56231 3845 53 52508 1.3 1 48489 4019 54 24641 1.3 1 21315 3326 55 74254 1.3 1 70600 3654 56 25401 1.3 1 22584 2817 57 31344 1.3 1 28789 2555 58 32212 1.3 1 29430 2782 59 69328 1.3 1 64760 4568 60 36835 1.3 1 34003 2832 61 27936 1.3 1 24840 3096 62 56041 1.3 1 53174 2867 63 18261 1.3 1 15839 2422 64 37267 1.3 1 34997 2270 65 19964 1.3 1 18138 1826 66 21905 1.3 1 19831 2074 67 26853 1.3 1 24771 2082 68 42734 1.3 1 40282 2452 69 33421 1.3 1 31241 2180 70 21025 1.3 1 19263 1762 71 37237 1.3 1 35500 1737 72 20523 1.3 1 18930 1593 73 21539 1.3 1 20186 1353 74 25956 1.3 1 24635 1321 75 25103 1.3 1 24150 953 76 10249 1.3 1 9634 615 77 2646 1.3 1 2268 378 78 3614 1.3 1 3232 382 79 6557 1.3 1 6082 475 80 8517 1.3 1 7990 527 81 9512 1.3 1 8939 573 82 9101 1.3 1 8448 653 83 8997 1.3 1 8400 597 84 8524 1.3 1 7882 642 85 7613 1.3 1 7071 542 86 6975 1.3 1 6462 513 87 6519 1.3 1 6100 419 88 6067 1.3 1 5644 423 89 5748 1.3 1 5342 406 90 5286 1.3 1 4903 383 91 4842 1.3 1 4496 346 92 4496 1.3 1 4126 370 93 4333 1.3 1 3997 336 94 3992 1.3 1 3593 399 95 3598 1.3 1 3360 238 96 3446 1.3 1 3207 239 97 3215 1.3 1 2926 289 98 2763 1.3 1 2592 171 99 2621 1.3 1 2385 236 100 2507 1.3 1 2346 161 101 2325 1.3 1 2084 241 102 2225 1.3 1 1917 308 103 1870 1.3 1 1718 152 104 1854 1.3 1 1627 227 105 1639 1.3 1 1469 170 106 1469 1.3 1 1307 162 107 1465 1.3 1 1298 167 108 1450 1.3 1 1256 194 109 1318 1.3 1 1136 182 110 1144 1.3 1 1000 144 111 1034 1.3 1 893 141 112 1018 1.3 1 824 194 113 902 1.3 1 713 189 114 839 1.3 1 732 107 115 800 1.3 1 685 115 116 777 1.3 1 660 117 117 799 1.3 1 656 143 118 862 1.3 1 600 262 119 648 1.3 1 546 102 120 715 1.3 1 586 129 121 669 1.3 1 512 157 122 645 1.3 1 501 144 123 670 1.3 1 509 161 124 600 1.3 1 495 105 125 676 1.3 1 548 128 126 738 1.3 1 617 121 127 768 1.3 1 647 121 128 770 1.3 1 664 106 129 944 1.3 1 788 156 130 946 1.3 1 842 104 131 1049 1.3 1 869 180 132 1160 1.3 1 1013 147 133 1424 1.3 1 1244 180 134 1970 1.3 1 1815 155 135 1701 1.3 1 1549 152 136 1731 1.3 1 1598 133 137 2230 1.3 1 2063 167 138 2364 1.3 1 2173 191 139 2142 1.3 1 2005 137 140 2645 1.3 1 2457 188 141 4135 1.3 1 3811 324 142 2241 1.3 1 2056 185 143 2492 1.3 1 2336 156 144 3051 1.3 1 2857 194 145 3435 1.3 1 3235 200 146 5604 1.3 1 5330 274 147 7102 1.3 1 6669 433 148 2054 1.3 1 1855 199 149 502 1.3 1 146 356 150 1876 1.3 1 1007 869 RUN STATISTICS FOR INPUT FILE: DE-1_trimmed_2.fastq.gz ============================================= 90005528 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 90005528 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1315155 (1.46%)