SUMMARISING RUN PARAMETERS ========================== Input filename: DE-6_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: 1913). Second best hit was Nextera (count: 10) 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-6_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 372.550 s (4.042 µs/read; 14.84 M reads/minute). === Summary === Total reads processed: 92,158,646 Reads with adapters: 27,062,079 (29.4%) Reads written (passing filters): 92,158,646 (100.0%) Total basepairs processed: 12,954,150,234 bp Quality-trimmed: 185,178,689 bp (1.4%) Total written (filtered): 12,394,720,898 bp (95.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 27062079 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.2% C: 32.9% G: 31.0% T: 10.8% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 10384591 23039661.5 0 10384591 2 5597311 5759915.4 0 5597311 3 943330 1439978.8 0 943330 4 103565 359994.7 0 103565 5 34832 89998.7 0 34832 6 9330 22499.7 0 9330 7 6151 5624.9 0 6151 8 3140 1406.2 0 3140 9 17020 351.6 0 11987 5033 10 10236 87.9 1 5400 4836 11 16752 22.0 1 7991 8761 12 23016 5.5 1 12630 10386 13 11169 1.4 1 4423 6746 14 17520 1.4 1 7849 9671 15 25726 1.4 1 12532 13194 16 25152 1.4 1 12179 12973 17 38414 1.4 1 23417 14997 18 51691 1.4 1 28998 22693 19 201996 1.4 1 154673 47323 20 74302 1.4 1 55977 18325 21 28136 1.4 1 16298 11838 22 35248 1.4 1 19067 16181 23 62624 1.4 1 35488 27136 24 706155 1.4 1 630953 75202 25 253703 1.4 1 215131 38572 26 300410 1.4 1 263156 37254 27 1847369 1.4 1 1769002 78367 28 230096 1.4 1 205975 24121 29 754408 1.4 1 722175 32233 30 146206 1.4 1 135447 10759 31 81423 1.4 1 71166 10257 32 410021 1.4 1 387916 22105 33 191928 1.4 1 169102 22826 34 1140574 1.4 1 1097493 43081 35 238302 1.4 1 216325 21977 36 712654 1.4 1 679623 33031 37 80923 1.4 1 71183 9740 38 126538 1.4 1 119378 7160 39 37331 1.4 1 31811 5520 40 162018 1.4 1 147296 14722 41 337142 1.4 1 317667 19475 42 64592 1.4 1 56475 8117 43 63769 1.4 1 56578 7191 44 54295 1.4 1 44661 9634 45 179511 1.4 1 167315 12196 46 58766 1.4 1 53294 5472 47 37794 1.4 1 33286 4508 48 8390 1.4 1 6749 1641 49 39382 1.4 1 35562 3820 50 106204 1.4 1 100392 5812 51 26187 1.4 1 22342 3845 52 58946 1.4 1 55149 3797 53 53275 1.4 1 49339 3936 54 22764 1.4 1 19501 3263 55 70312 1.4 1 66765 3547 56 24348 1.4 1 21766 2582 57 27461 1.4 1 25157 2304 58 30724 1.4 1 28269 2455 59 61696 1.4 1 57662 4034 60 33227 1.4 1 30585 2642 61 23998 1.4 1 21300 2698 62 47042 1.4 1 44631 2411 63 15283 1.4 1 13261 2022 64 29222 1.4 1 27337 1885 65 16076 1.4 1 14546 1530 66 16865 1.4 1 15222 1643 67 20159 1.4 1 18567 1592 68 32240 1.4 1 30449 1791 69 25087 1.4 1 23407 1680 70 14657 1.4 1 13365 1292 71 27046 1.4 1 25835 1211 72 14386 1.4 1 13252 1134 73 14280 1.4 1 13379 901 74 17409 1.4 1 16558 851 75 17008 1.4 1 16302 706 76 7099 1.4 1 6676 423 77 1860 1.4 1 1582 278 78 2400 1.4 1 2119 281 79 4344 1.4 1 3985 359 80 5626 1.4 1 5251 375 81 6115 1.4 1 5760 355 82 5948 1.4 1 5500 448 83 5873 1.4 1 5423 450 84 5588 1.4 1 5209 379 85 4938 1.4 1 4547 391 86 4531 1.4 1 4184 347 87 4094 1.4 1 3793 301 88 3894 1.4 1 3532 362 89 3810 1.4 1 3565 245 90 3508 1.4 1 3265 243 91 3289 1.4 1 3016 273 92 3209 1.4 1 2960 249 93 2899 1.4 1 2655 244 94 2720 1.4 1 2483 237 95 2356 1.4 1 2196 160 96 2402 1.4 1 2229 173 97 2263 1.4 1 2071 192 98 2048 1.4 1 1911 137 99 1983 1.4 1 1763 220 100 1857 1.4 1 1725 132 101 1865 1.4 1 1667 198 102 1741 1.4 1 1550 191 103 1563 1.4 1 1429 134 104 1515 1.4 1 1346 169 105 1358 1.4 1 1217 141 106 1189 1.4 1 1101 88 107 1248 1.4 1 1097 151 108 1134 1.4 1 1008 126 109 1144 1.4 1 993 151 110 977 1.4 1 870 107 111 1000 1.4 1 868 132 112 994 1.4 1 854 140 113 860 1.4 1 727 133 114 905 1.4 1 779 126 115 819 1.4 1 733 86 116 905 1.4 1 796 109 117 866 1.4 1 740 126 118 938 1.4 1 753 185 119 869 1.4 1 757 112 120 856 1.4 1 730 126 121 828 1.4 1 711 117 122 878 1.4 1 766 112 123 1017 1.4 1 880 137 124 991 1.4 1 892 99 125 1115 1.4 1 960 155 126 1287 1.4 1 1135 152 127 1423 1.4 1 1309 114 128 1475 1.4 1 1317 158 129 1793 1.4 1 1614 179 130 1925 1.4 1 1750 175 131 2054 1.4 1 1883 171 132 2411 1.4 1 2204 207 133 2650 1.4 1 2430 220 134 3512 1.4 1 3287 225 135 3465 1.4 1 3239 226 136 3601 1.4 1 3372 229 137 4299 1.4 1 4018 281 138 4666 1.4 1 4406 260 139 4447 1.4 1 4090 357 140 5505 1.4 1 5118 387 141 8219 1.4 1 7662 557 142 4481 1.4 1 4241 240 143 5178 1.4 1 4870 308 144 6323 1.4 1 5989 334 145 7632 1.4 1 7242 390 146 11763 1.4 1 11191 572 147 13809 1.4 1 13049 760 148 4193 1.4 1 3871 322 149 676 1.4 1 270 406 150 2209 1.4 1 1153 1056 RUN STATISTICS FOR INPUT FILE: DE-6_trimmed_2.fastq.gz ============================================= 92158646 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 92158646 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1567889 (1.70%)