SUMMARISING RUN PARAMETERS ========================== Input filename: DE-4_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: 2611). Second best hit was smallRNA (count: 11) 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-4_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 408.471 s (4.248 µs/read; 14.12 M reads/minute). === Summary === Total reads processed: 96,145,572 Reads with adapters: 25,979,656 (27.0%) Reads written (passing filters): 96,145,572 (100.0%) Total basepairs processed: 13,632,918,494 bp Quality-trimmed: 173,261,372 bp (1.3%) Total written (filtered): 13,122,172,108 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25979656 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.0% C: 34.1% G: 29.6% T: 11.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 10415808 24036393.0 0 10415808 2 5318917 6009098.2 0 5318917 3 935287 1502274.6 0 935287 4 106015 375568.6 0 106015 5 35981 93892.2 0 35981 6 9778 23473.0 0 9778 7 5969 5868.3 0 5969 8 2995 1467.1 0 2995 9 15998 366.8 0 11413 4585 10 9740 91.7 1 5263 4477 11 15320 22.9 1 7214 8106 12 22783 5.7 1 12210 10573 13 10164 1.4 1 3762 6402 14 17661 1.4 1 7589 10072 15 24936 1.4 1 11960 12976 16 22314 1.4 1 10507 11807 17 36097 1.4 1 21566 14531 18 44797 1.4 1 24567 20230 19 176895 1.4 1 134566 42329 20 66216 1.4 1 49386 16830 21 27015 1.4 1 15147 11868 22 33988 1.4 1 17724 16264 23 59499 1.4 1 32808 26691 24 708971 1.4 1 634636 74335 25 261661 1.4 1 222108 39553 26 295306 1.4 1 259597 35709 27 1707452 1.4 1 1635110 72342 28 201366 1.4 1 179944 21422 29 639921 1.4 1 612508 27413 30 126642 1.4 1 117064 9578 31 85841 1.4 1 75448 10393 32 420128 1.4 1 397603 22525 33 173074 1.4 1 151751 21323 34 1075265 1.4 1 1034306 40959 35 230025 1.4 1 209379 20646 36 631885 1.4 1 602763 29122 37 74545 1.4 1 65822 8723 38 113793 1.4 1 107382 6411 39 35751 1.4 1 30870 4881 40 136614 1.4 1 123946 12668 41 302967 1.4 1 285735 17232 42 49874 1.4 1 43198 6676 43 57745 1.4 1 51500 6245 44 48836 1.4 1 40026 8810 45 160825 1.4 1 150137 10688 46 46367 1.4 1 41833 4534 47 36473 1.4 1 32395 4078 48 7369 1.4 1 5920 1449 49 30397 1.4 1 27382 3015 50 91390 1.4 1 86302 5088 51 24680 1.4 1 21024 3656 52 53220 1.4 1 49913 3307 53 44100 1.4 1 40523 3577 54 21246 1.4 1 18476 2770 55 62355 1.4 1 59236 3119 56 19643 1.4 1 17414 2229 57 25077 1.4 1 23024 2053 58 23901 1.4 1 21769 2132 59 56796 1.4 1 53108 3688 60 28533 1.4 1 26128 2405 61 21244 1.4 1 18951 2293 62 41029 1.4 1 38879 2150 63 12686 1.4 1 11011 1675 64 27227 1.4 1 25569 1658 65 13533 1.4 1 12201 1332 66 14905 1.4 1 13467 1438 67 18014 1.4 1 16633 1381 68 28829 1.4 1 27155 1674 69 21718 1.4 1 20255 1463 70 14355 1.4 1 13150 1205 71 23516 1.4 1 22434 1082 72 12672 1.4 1 11603 1069 73 13636 1.4 1 12770 866 74 16045 1.4 1 15232 813 75 15075 1.4 1 14449 626 76 5573 1.4 1 5185 388 77 1577 1.4 1 1322 255 78 2067 1.4 1 1806 261 79 3841 1.4 1 3523 318 80 4926 1.4 1 4621 305 81 5438 1.4 1 5098 340 82 5260 1.4 1 4890 370 83 4967 1.4 1 4589 378 84 4741 1.4 1 4378 363 85 4166 1.4 1 3831 335 86 3850 1.4 1 3544 306 87 3721 1.4 1 3438 283 88 3487 1.4 1 3253 234 89 3247 1.4 1 2991 256 90 2922 1.4 1 2678 244 91 2861 1.4 1 2625 236 92 2803 1.4 1 2560 243 93 2689 1.4 1 2436 253 94 2493 1.4 1 2225 268 95 2241 1.4 1 2086 155 96 2169 1.4 1 2012 157 97 2115 1.4 1 1921 194 98 1853 1.4 1 1706 147 99 1759 1.4 1 1584 175 100 1623 1.4 1 1490 133 101 1548 1.4 1 1396 152 102 1612 1.4 1 1398 214 103 1344 1.4 1 1227 117 104 1273 1.4 1 1145 128 105 1239 1.4 1 1108 131 106 1023 1.4 1 931 92 107 1179 1.4 1 1048 131 108 985 1.4 1 874 111 109 1006 1.4 1 882 124 110 877 1.4 1 778 99 111 788 1.4 1 687 101 112 802 1.4 1 666 136 113 693 1.4 1 562 131 114 637 1.4 1 575 62 115 649 1.4 1 563 86 116 622 1.4 1 547 75 117 628 1.4 1 532 96 118 669 1.4 1 520 149 119 585 1.4 1 491 94 120 572 1.4 1 506 66 121 600 1.4 1 486 114 122 568 1.4 1 477 91 123 638 1.4 1 512 126 124 610 1.4 1 530 80 125 644 1.4 1 541 103 126 710 1.4 1 618 92 127 775 1.4 1 693 82 128 866 1.4 1 767 99 129 1041 1.4 1 876 165 130 1041 1.4 1 956 85 131 1145 1.4 1 1001 144 132 1353 1.4 1 1222 131 133 1592 1.4 1 1403 189 134 1905 1.4 1 1752 153 135 1873 1.4 1 1700 173 136 2006 1.4 1 1853 153 137 2374 1.4 1 2180 194 138 2583 1.4 1 2401 182 139 2340 1.4 1 2200 140 140 3005 1.4 1 2783 222 141 4178 1.4 1 3878 300 142 2390 1.4 1 2203 187 143 2700 1.4 1 2515 185 144 3239 1.4 1 3076 163 145 3812 1.4 1 3604 208 146 5869 1.4 1 5562 307 147 6944 1.4 1 6547 397 148 1817 1.4 1 1657 160 149 307 1.4 1 121 186 150 920 1.4 1 558 362 RUN STATISTICS FOR INPUT FILE: DE-4_trimmed_2.fastq.gz ============================================= 96145572 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 96145572 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 728293 (0.76%)