SUMMARISING RUN PARAMETERS ========================== Input filename: DE-6_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: 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_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 399.308 s (4.333 µs/read; 13.85 M reads/minute). === Summary === Total reads processed: 92,158,646 Reads with adapters: 18,268,129 (19.8%) Reads written (passing filters): 92,158,646 (100.0%) Total basepairs processed: 12,540,939,221 bp Quality-trimmed: 90,065,484 bp (0.7%) Total written (filtered): 12,257,227,602 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18268129 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.8% C: 35.1% G: 14.4% T: 12.0% none/other: 5.8% Overview of removed sequences length count expect max.err error counts 1 11347689 23039661.5 0 11347689 2 4643501 5759915.4 0 4643501 3 698095 1439978.8 0 698095 4 97878 359994.7 0 97878 5 42575 89998.7 0 42575 6 5875 22499.7 0 5875 7 2372 5624.9 0 2372 8 368 1406.2 0 368 9 3969 351.6 0 2058 1911 10 1521 87.9 1 387 1134 11 4451 22.0 1 416 4035 12 4456 5.5 1 211 4245 13 1873 1.4 1 645 1228 14 7063 1.4 1 480 6583 15 3934 1.4 1 725 3209 16 6528 1.4 1 1090 5438 17 7844 1.4 1 1509 6335 18 5341 1.4 1 1450 3891 19 7451 1.4 1 1992 5459 20 6742 1.4 1 1912 4830 21 10376 1.4 1 3890 6486 22 6596 1.4 1 2409 4187 23 4639 1.4 1 1457 3182 24 7322 1.4 1 3283 4039 25 6505 1.4 1 2728 3777 26 8361 1.4 1 3989 4372 27 19493 1.4 1 9836 9657 28 8460 1.4 1 2294 6166 29 6471 1.4 1 2480 3991 30 5919 1.4 1 3451 2468 31 14031 1.4 1 8728 5303 32 6009 1.4 1 1978 4031 33 11222 1.4 1 6143 5079 34 8523 1.4 1 4816 3707 35 9879 1.4 1 5408 4471 36 14345 1.4 1 8698 5647 37 13842 1.4 1 8210 5632 38 6706 1.4 1 2283 4423 39 6309 1.4 1 2748 3561 40 5495 1.4 1 3447 2048 41 11211 1.4 1 7007 4204 42 4307 1.4 1 1494 2813 43 12048 1.4 1 6741 5307 44 3898 1.4 1 1958 1940 45 7278 1.4 1 4140 3138 46 6565 1.4 1 3732 2833 47 6363 1.4 1 3820 2543 48 7502 1.4 1 4353 3149 49 7117 1.4 1 4059 3058 50 6983 1.4 1 3946 3037 51 6811 1.4 1 3796 3015 52 6782 1.4 1 3931 2851 53 6341 1.4 1 3671 2670 54 6568 1.4 1 3783 2785 55 6952 1.4 1 4091 2861 56 6698 1.4 1 3910 2788 57 5421 1.4 1 3040 2381 58 3795 1.4 1 2090 1705 59 2509 1.4 1 1342 1167 60 1546 1.4 1 792 754 61 953 1.4 1 550 403 62 710 1.4 1 417 293 63 715 1.4 1 381 334 64 563 1.4 1 304 259 65 494 1.4 1 261 233 66 538 1.4 1 296 242 67 729 1.4 1 408 321 68 914 1.4 1 521 393 69 946 1.4 1 545 401 70 956 1.4 1 523 433 71 893 1.4 1 512 381 72 900 1.4 1 497 403 73 815 1.4 1 438 377 74 740 1.4 1 395 345 75 718 1.4 1 380 338 76 694 1.4 1 371 323 77 618 1.4 1 310 308 78 543 1.4 1 281 262 79 572 1.4 1 242 330 80 547 1.4 1 249 298 81 552 1.4 1 177 375 82 486 1.4 1 184 302 83 460 1.4 1 160 300 84 408 1.4 1 155 253 85 360 1.4 1 130 230 86 318 1.4 1 97 221 87 328 1.4 1 111 217 88 377 1.4 1 134 243 89 302 1.4 1 121 181 90 289 1.4 1 219 70 91 255 1.4 1 175 80 92 244 1.4 1 158 86 93 240 1.4 1 170 70 94 236 1.4 1 137 99 95 222 1.4 1 133 89 96 191 1.4 1 124 67 97 204 1.4 1 99 105 98 165 1.4 1 89 76 99 200 1.4 1 100 100 100 152 1.4 1 89 63 101 130 1.4 1 79 51 102 136 1.4 1 65 71 103 122 1.4 1 63 59 104 124 1.4 1 66 58 105 74 1.4 1 37 37 106 80 1.4 1 22 58 107 95 1.4 1 23 72 108 91 1.4 1 21 70 109 61 1.4 1 16 45 110 66 1.4 1 20 46 111 73 1.4 1 15 58 112 64 1.4 1 12 52 113 47 1.4 1 9 38 114 68 1.4 1 9 59 115 55 1.4 1 17 38 116 59 1.4 1 14 45 117 78 1.4 1 16 62 118 77 1.4 1 16 61 119 70 1.4 1 19 51 120 86 1.4 1 15 71 121 75 1.4 1 12 63 122 65 1.4 1 11 54 123 72 1.4 1 12 60 124 79 1.4 1 13 66 125 62 1.4 1 23 39 126 64 1.4 1 15 49 127 102 1.4 1 24 78 128 113 1.4 1 27 86 129 97 1.4 1 34 63 130 93 1.4 1 29 64 131 115 1.4 1 38 77 132 130 1.4 1 56 74 133 135 1.4 1 54 81 134 157 1.4 1 63 94 135 165 1.4 1 46 119 136 185 1.4 1 61 124 137 178 1.4 1 81 97 138 172 1.4 1 77 95 139 198 1.4 1 85 113 140 299 1.4 1 141 158 141 383 1.4 1 208 175 142 236 1.4 1 109 127 143 268 1.4 1 110 158 144 362 1.4 1 158 204 145 400 1.4 1 167 233 146 541 1.4 1 253 288 147 881 1.4 1 269 612 148 721 1.4 1 96 625 149 10970 1.4 1 2 10968 150 1021884 1.4 1 24 1021860 RUN STATISTICS FOR INPUT FILE: DE-6_trimmed_1.fastq.gz ============================================= 92158646 sequences processed in total