SUMMARISING RUN PARAMETERS ========================== Input filename: DE-7_trimmed_1.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: 2268). Second best hit was smallRNA (count: 23) 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-7_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 299.566 s (4.265 µs/read; 14.07 M reads/minute). === Summary === Total reads processed: 70,236,818 Reads with adapters: 13,290,952 (18.9%) Reads written (passing filters): 70,236,818 (100.0%) Total basepairs processed: 9,682,289,667 bp Quality-trimmed: 64,669,067 bp (0.7%) Total written (filtered): 9,550,644,657 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13290952 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.7% C: 35.2% G: 18.4% T: 12.8% none/other: 1.9% Overview of removed sequences length count expect max.err error counts 1 8051605 17559204.5 0 8051605 2 3916486 4389801.1 0 3916486 3 605236 1097450.3 0 605236 4 87639 274362.6 0 87639 5 37807 68590.6 0 37807 6 6043 17147.7 0 6043 7 2441 4286.9 0 2441 8 247 1071.7 0 247 9 3835 267.9 0 1609 2226 10 1068 67.0 1 236 832 11 3504 16.7 1 272 3232 12 4609 4.2 1 139 4470 13 1265 1.0 1 329 936 14 7249 1.0 1 391 6858 15 2546 1.0 1 446 2100 16 5683 1.0 1 829 4854 17 6912 1.0 1 1301 5611 18 5058 1.0 1 1300 3758 19 7099 1.0 1 1937 5162 20 6447 1.0 1 1933 4514 21 10047 1.0 1 3831 6216 22 6287 1.0 1 2475 3812 23 3671 1.0 1 1213 2458 24 6950 1.0 1 3222 3728 25 6667 1.0 1 3037 3630 26 7944 1.0 1 4075 3869 27 19539 1.0 1 10245 9294 28 6367 1.0 1 1756 4611 29 5740 1.0 1 2240 3500 30 6390 1.0 1 3807 2583 31 13633 1.0 1 8617 5016 32 4043 1.0 1 1476 2567 33 10274 1.0 1 5890 4384 34 13252 1.0 1 8062 5190 35 8380 1.0 1 4798 3582 36 4326 1.0 1 1768 2558 37 7385 1.0 1 4456 2929 38 6551 1.0 1 4054 2497 39 7123 1.0 1 4097 3026 40 8062 1.0 1 4741 3321 41 10966 1.0 1 6817 4149 42 3378 1.0 1 1373 2005 43 9383 1.0 1 5475 3908 44 3718 1.0 1 2215 1503 45 5810 1.0 1 3450 2360 46 5689 1.0 1 3461 2228 47 5225 1.0 1 3317 1908 48 5751 1.0 1 3555 2196 49 5581 1.0 1 3372 2209 50 5422 1.0 1 3316 2106 51 5263 1.0 1 3205 2058 52 5355 1.0 1 3228 2127 53 4863 1.0 1 2850 2013 54 4954 1.0 1 2996 1958 55 5061 1.0 1 3059 2002 56 4989 1.0 1 3050 1939 57 4312 1.0 1 2515 1797 58 3137 1.0 1 1827 1310 59 2252 1.0 1 1292 960 60 1471 1.0 1 801 670 61 1194 1.0 1 702 492 62 992 1.0 1 601 391 63 903 1.0 1 556 347 64 676 1.0 1 384 292 65 644 1.0 1 386 258 66 739 1.0 1 444 295 67 845 1.0 1 538 307 68 862 1.0 1 536 326 69 935 1.0 1 557 378 70 927 1.0 1 521 406 71 820 1.0 1 473 347 72 801 1.0 1 469 332 73 661 1.0 1 375 286 74 654 1.0 1 373 281 75 594 1.0 1 323 271 76 607 1.0 1 347 260 77 518 1.0 1 280 238 78 424 1.0 1 218 206 79 432 1.0 1 215 217 80 467 1.0 1 195 272 81 460 1.0 1 179 281 82 401 1.0 1 155 246 83 381 1.0 1 170 211 84 303 1.0 1 110 193 85 330 1.0 1 136 194 86 293 1.0 1 117 176 87 282 1.0 1 121 161 88 258 1.0 1 93 165 89 238 1.0 1 108 130 90 242 1.0 1 146 96 91 241 1.0 1 152 89 92 214 1.0 1 140 74 93 207 1.0 1 131 76 94 176 1.0 1 105 71 95 173 1.0 1 104 69 96 171 1.0 1 97 74 97 139 1.0 1 72 67 98 168 1.0 1 72 96 99 139 1.0 1 72 67 100 137 1.0 1 73 64 101 110 1.0 1 54 56 102 113 1.0 1 48 65 103 84 1.0 1 39 45 104 102 1.0 1 50 52 105 98 1.0 1 53 45 106 68 1.0 1 19 49 107 70 1.0 1 14 56 108 77 1.0 1 21 56 109 55 1.0 1 13 42 110 65 1.0 1 19 46 111 52 1.0 1 10 42 112 54 1.0 1 13 41 113 57 1.0 1 16 41 114 62 1.0 1 12 50 115 48 1.0 1 18 30 116 66 1.0 1 11 55 117 62 1.0 1 15 47 118 78 1.0 1 12 66 119 54 1.0 1 9 45 120 75 1.0 1 12 63 121 66 1.0 1 16 50 122 46 1.0 1 8 38 123 48 1.0 1 14 34 124 61 1.0 1 23 38 125 44 1.0 1 8 36 126 79 1.0 1 31 48 127 74 1.0 1 24 50 128 78 1.0 1 23 55 129 68 1.0 1 21 47 130 87 1.0 1 38 49 131 106 1.0 1 49 57 132 108 1.0 1 54 54 133 151 1.0 1 66 85 134 138 1.0 1 51 87 135 169 1.0 1 67 102 136 146 1.0 1 74 72 137 157 1.0 1 79 78 138 167 1.0 1 97 70 139 167 1.0 1 73 94 140 207 1.0 1 98 109 141 255 1.0 1 132 123 142 129 1.0 1 50 79 143 160 1.0 1 76 84 144 177 1.0 1 79 98 145 202 1.0 1 102 100 146 276 1.0 1 139 137 147 387 1.0 1 152 235 148 192 1.0 1 21 171 149 3174 1.0 1 1 3173 150 234745 1.0 1 11 234734 RUN STATISTICS FOR INPUT FILE: DE-7_trimmed_1.fastq.gz ============================================= 70236818 sequences processed in total