SUMMARISING RUN PARAMETERS ========================== Input filename: DE-3C_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: 2019). Second best hit was Nextera (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-3C_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 345.093 s (4.267 µs/read; 14.06 M reads/minute). === Summary === Total reads processed: 80,872,082 Reads with adapters: 21,841,870 (27.0%) Reads written (passing filters): 80,872,082 (100.0%) Total basepairs processed: 11,460,845,031 bp Quality-trimmed: 144,355,118 bp (1.3%) Total written (filtered): 11,034,525,787 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21841870 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.9% C: 34.2% G: 30.1% T: 10.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 8696156 20218020.5 0 8696156 2 4533952 5054505.1 0 4533952 3 795505 1263626.3 0 795505 4 88308 315906.6 0 88308 5 30440 78976.6 0 30440 6 8528 19744.2 0 8528 7 5276 4936.0 0 5276 8 2593 1234.0 0 2593 9 13429 308.5 0 9449 3980 10 8241 77.1 1 4359 3882 11 13244 19.3 1 6232 7012 12 19114 4.8 1 10263 8851 13 9066 1.2 1 3341 5725 14 15078 1.2 1 6522 8556 15 21087 1.2 1 10128 10959 16 19192 1.2 1 8977 10215 17 31014 1.2 1 18491 12523 18 40079 1.2 1 21892 18187 19 154703 1.2 1 117376 37327 20 57733 1.2 1 42887 14846 21 23151 1.2 1 13178 9973 22 29156 1.2 1 15260 13896 23 51319 1.2 1 28422 22897 24 580248 1.2 1 518173 62075 25 212636 1.2 1 180196 32440 26 246845 1.2 1 216154 30691 27 1445131 1.2 1 1383915 61216 28 177735 1.2 1 158948 18787 29 571344 1.2 1 546873 24471 30 111477 1.2 1 103216 8261 31 70176 1.2 1 61478 8698 32 346776 1.2 1 328066 18710 33 149012 1.2 1 130848 18164 34 883300 1.2 1 848991 34309 35 188153 1.2 1 170899 17254 36 536192 1.2 1 511198 24994 37 62401 1.2 1 54728 7673 38 96190 1.2 1 90573 5617 39 29179 1.2 1 24941 4238 40 118039 1.2 1 107374 10665 41 252851 1.2 1 238335 14516 42 44972 1.2 1 38969 6003 43 48350 1.2 1 43129 5221 44 41567 1.2 1 34086 7481 45 134589 1.2 1 125582 9007 46 40857 1.2 1 36909 3948 47 28966 1.2 1 25655 3311 48 5970 1.2 1 4770 1200 49 26591 1.2 1 23965 2626 50 75610 1.2 1 71476 4134 51 20164 1.2 1 17156 3008 52 43262 1.2 1 40565 2697 53 36642 1.2 1 33767 2875 54 17015 1.2 1 14688 2327 55 51687 1.2 1 49023 2664 56 16670 1.2 1 14828 1842 57 20039 1.2 1 18295 1744 58 20579 1.2 1 18864 1715 59 43986 1.2 1 41100 2886 60 23413 1.2 1 21527 1886 61 16778 1.2 1 14899 1879 62 33136 1.2 1 31320 1816 63 10280 1.2 1 8943 1337 64 20589 1.2 1 19280 1309 65 11016 1.2 1 9953 1063 66 11869 1.2 1 10701 1168 67 13785 1.2 1 12650 1135 68 22133 1.2 1 20804 1329 69 16982 1.2 1 15917 1065 70 10266 1.2 1 9358 908 71 18067 1.2 1 17206 861 72 9719 1.2 1 8877 842 73 10040 1.2 1 9429 611 74 11829 1.2 1 11221 608 75 11324 1.2 1 10817 507 76 4609 1.2 1 4311 298 77 1171 1.2 1 944 227 78 1570 1.2 1 1363 207 79 2830 1.2 1 2571 259 80 3871 1.2 1 3589 282 81 4032 1.2 1 3753 279 82 3952 1.2 1 3681 271 83 3864 1.2 1 3553 311 84 3665 1.2 1 3374 291 85 3324 1.2 1 3047 277 86 3126 1.2 1 2806 320 87 2853 1.2 1 2672 181 88 2686 1.2 1 2463 223 89 2620 1.2 1 2404 216 90 2486 1.2 1 2262 224 91 2289 1.2 1 2070 219 92 2172 1.2 1 1980 192 93 2011 1.2 1 1795 216 94 1929 1.2 1 1689 240 95 1693 1.2 1 1576 117 96 1643 1.2 1 1488 155 97 1568 1.2 1 1396 172 98 1418 1.2 1 1296 122 99 1436 1.2 1 1269 167 100 1349 1.2 1 1238 111 101 1250 1.2 1 1108 142 102 1292 1.2 1 1096 196 103 1029 1.2 1 926 103 104 1156 1.2 1 996 160 105 954 1.2 1 837 117 106 851 1.2 1 745 106 107 864 1.2 1 759 105 108 816 1.2 1 688 128 109 868 1.2 1 702 166 110 727 1.2 1 634 93 111 651 1.2 1 574 77 112 709 1.2 1 555 154 113 616 1.2 1 495 121 114 532 1.2 1 461 71 115 561 1.2 1 467 94 116 521 1.2 1 456 65 117 535 1.2 1 451 84 118 604 1.2 1 440 164 119 449 1.2 1 363 86 120 521 1.2 1 435 86 121 511 1.2 1 400 111 122 521 1.2 1 424 97 123 508 1.2 1 417 91 124 492 1.2 1 421 71 125 524 1.2 1 438 86 126 576 1.2 1 474 102 127 628 1.2 1 556 72 128 728 1.2 1 628 100 129 898 1.2 1 755 143 130 769 1.2 1 673 96 131 830 1.2 1 740 90 132 1007 1.2 1 890 117 133 1217 1.2 1 1085 132 134 1522 1.2 1 1403 119 135 1428 1.2 1 1323 105 136 1527 1.2 1 1420 107 137 1827 1.2 1 1685 142 138 2020 1.2 1 1854 166 139 1920 1.2 1 1795 125 140 2213 1.2 1 2041 172 141 3467 1.2 1 3226 241 142 1926 1.2 1 1788 138 143 2145 1.2 1 1996 149 144 2724 1.2 1 2574 150 145 3189 1.2 1 3017 172 146 5078 1.2 1 4833 245 147 5916 1.2 1 5549 367 148 1819 1.2 1 1678 141 149 313 1.2 1 125 188 150 1163 1.2 1 710 453 RUN STATISTICS FOR INPUT FILE: DE-3C_trimmed_2.fastq.gz ============================================= 80872082 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 80872082 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 734473 (0.91%)