SUMMARISING RUN PARAMETERS ========================== Input filename: HB_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: 2731). Second best hit was smallRNA (count: 17) 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 HB_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 324.225 s (4.081 µs/read; 14.70 M reads/minute). === Summary === Total reads processed: 79,451,611 Reads with adapters: 15,999,273 (20.1%) Reads written (passing filters): 79,451,611 (100.0%) Total basepairs processed: 10,724,628,959 bp Quality-trimmed: 77,403,897 bp (0.7%) Total written (filtered): 10,297,575,751 bp (96.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15999273 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.3% C: 32.0% G: 15.8% T: 10.9% none/other: 12.9% Overview of removed sequences length count expect max.err error counts 1 8799223 19862902.8 0 8799223 2 3911152 4965725.7 0 3911152 3 617591 1241431.4 0 617591 4 85277 310357.9 0 85277 5 37858 77589.5 0 37858 6 5760 19397.4 0 5760 7 2218 4849.3 0 2218 8 284 1212.3 0 284 9 4006 303.1 0 1757 2249 10 1136 75.8 1 311 825 11 3449 18.9 1 318 3131 12 4827 4.7 1 144 4683 13 1361 1.2 1 510 851 14 7360 1.2 1 321 7039 15 2396 1.2 1 518 1878 16 5675 1.2 1 785 4890 17 6307 1.2 1 1225 5082 18 4912 1.2 1 1155 3757 19 6615 1.2 1 1860 4755 20 6334 1.2 1 1783 4551 21 9830 1.2 1 3412 6418 22 6173 1.2 1 2167 4006 23 3697 1.2 1 1133 2564 24 6856 1.2 1 2872 3984 25 6083 1.2 1 2553 3530 26 7377 1.2 1 3206 4171 27 18248 1.2 1 8523 9725 28 6201 1.2 1 1818 4383 29 5717 1.2 1 2201 3516 30 5751 1.2 1 3164 2587 31 12813 1.2 1 7408 5405 32 4335 1.2 1 1457 2878 33 10781 1.2 1 5772 5009 34 7373 1.2 1 3843 3530 35 8247 1.2 1 4463 3784 36 8933 1.2 1 4747 4186 37 8897 1.2 1 4597 4300 38 8502 1.2 1 4306 4196 39 14552 1.2 1 7613 6939 40 8631 1.2 1 4529 4102 41 11571 1.2 1 5421 6150 42 5192 1.2 1 1872 3320 43 11238 1.2 1 5620 5618 44 5497 1.2 1 2896 2601 45 7823 1.2 1 4155 3668 46 7553 1.2 1 4054 3499 47 7774 1.2 1 4211 3563 48 8861 1.2 1 4797 4064 49 9132 1.2 1 4769 4363 50 9041 1.2 1 4712 4329 51 9286 1.2 1 4868 4418 52 9380 1.2 1 4859 4521 53 9399 1.2 1 4911 4488 54 9470 1.2 1 5014 4456 55 10332 1.2 1 5695 4637 56 11245 1.2 1 6130 5115 57 11283 1.2 1 6135 5148 58 9324 1.2 1 4985 4339 59 7088 1.2 1 3755 3333 60 4712 1.2 1 2403 2309 61 3355 1.2 1 1779 1576 62 2735 1.2 1 1458 1277 63 2434 1.2 1 1348 1086 64 1912 1.2 1 1044 868 65 1773 1.2 1 982 791 66 2029 1.2 1 1185 844 67 2349 1.2 1 1363 986 68 2753 1.2 1 1530 1223 69 3071 1.2 1 1756 1315 70 3062 1.2 1 1736 1326 71 3134 1.2 1 1682 1452 72 2922 1.2 1 1575 1347 73 2790 1.2 1 1529 1261 74 2680 1.2 1 1460 1220 75 2609 1.2 1 1437 1172 76 2240 1.2 1 1178 1062 77 2246 1.2 1 1158 1088 78 2106 1.2 1 1121 985 79 2012 1.2 1 963 1049 80 2093 1.2 1 923 1170 81 1942 1.2 1 793 1149 82 1903 1.2 1 776 1127 83 1739 1.2 1 716 1023 84 1604 1.2 1 684 920 85 1380 1.2 1 589 791 86 1321 1.2 1 513 808 87 1158 1.2 1 500 658 88 1119 1.2 1 453 666 89 1172 1.2 1 549 623 90 1108 1.2 1 756 352 91 989 1.2 1 664 325 92 894 1.2 1 627 267 93 854 1.2 1 571 283 94 704 1.2 1 463 241 95 641 1.2 1 424 217 96 565 1.2 1 393 172 97 508 1.2 1 321 187 98 544 1.2 1 346 198 99 465 1.2 1 303 162 100 391 1.2 1 241 150 101 338 1.2 1 216 122 102 311 1.2 1 195 116 103 284 1.2 1 188 96 104 263 1.2 1 160 103 105 214 1.2 1 104 110 106 174 1.2 1 79 95 107 169 1.2 1 64 105 108 152 1.2 1 45 107 109 131 1.2 1 61 70 110 102 1.2 1 36 66 111 103 1.2 1 39 64 112 91 1.2 1 27 64 113 83 1.2 1 31 52 114 119 1.2 1 36 83 115 72 1.2 1 28 44 116 118 1.2 1 23 95 117 108 1.2 1 22 86 118 137 1.2 1 37 100 119 105 1.2 1 32 73 120 106 1.2 1 18 88 121 92 1.2 1 13 79 122 96 1.2 1 27 69 123 140 1.2 1 29 111 124 86 1.2 1 21 65 125 101 1.2 1 31 70 126 136 1.2 1 32 104 127 123 1.2 1 36 87 128 139 1.2 1 57 82 129 131 1.2 1 36 95 130 129 1.2 1 47 82 131 201 1.2 1 76 125 132 157 1.2 1 56 101 133 193 1.2 1 57 136 134 265 1.2 1 115 150 135 241 1.2 1 102 139 136 255 1.2 1 101 154 137 301 1.2 1 108 193 138 339 1.2 1 143 196 139 326 1.2 1 133 193 140 445 1.2 1 192 253 141 624 1.2 1 285 339 142 345 1.2 1 117 228 143 461 1.2 1 190 271 144 586 1.2 1 243 343 145 632 1.2 1 215 417 146 966 1.2 1 428 538 147 1655 1.2 1 543 1112 148 1307 1.2 1 179 1128 149 22695 1.2 1 14 22681 150 2033681 1.2 1 139 2033542 RUN STATISTICS FOR INPUT FILE: HB_trimmed_1.fastq.gz ============================================= 79451611 sequences processed in total